diff --git a/README.md b/README.md
index 2105789..d36f1a0 100644
--- a/README.md
+++ b/README.md
@@ -88,4 +88,60 @@ npm install suspicious-package --safe-chain-malware-action=prompt
 
 # Usage in CI/CD
 
-[Learn more about Safe Chain CI/CD integration in the Aikido docs.](https://help.aikido.dev/code-scanning/aikido-malware-scanning/malware-scanning-with-safe-chain-in-ci-cd-environments)
+You can protect your CI/CD pipelines from malicious packages by integrating Aikido Safe Chain into your build process. This ensures that any packages installed during your automated builds are checked for malware before installation.
+
+For optimal protection in CI/CD environments, we recommend using **npm >= 10.4.0** as it provides full dependency tree scanning. Other package managers currently offer limited scanning of install command arguments only.
+
+## Setup
+
+To use Aikido Safe Chain in CI/CD environments, run the following command after installing the package:
+
+```shell
+safe-chain setup-ci
+```
+
+This automatically configures your CI environment to use Aikido Safe Chain for all package manager commands.
+
+## Supported Platforms
+
+- ✅ **GitHub Actions**
+- ✅ **Azure Pipelines**
+
+## GitHub Actions Example
+
+```yaml
+- name: Setup Node.js
+  uses: actions/setup-node@v4
+  with:
+    node-version: "22"
+    cache: "npm"
+
+- name: Setup safe-chain
+  run: |
+    npm i -g @aikidosec/safe-chain
+    safe-chain setup-ci
+
+- name: Install dependencies
+  run: |
+    npm ci
+```
+
+## Azure DevOps Example
+
+```yaml
+- task: NodeTool@0
+  inputs:
+    versionSpec: "22.x"
+  displayName: "Install Node.js"
+
+- script: |
+    npm i -g @aikidosec/safe-chain
+    safe-chain setup-ci
+  displayName: "Install safe chain"
+
+- script: |
+    npm ci
+  displayName: "npm install and build"
+```
+
+After setup, all subsequent package manager commands in your CI pipeline will automatically be protected by Aikido Safe Chain's malware detection.
diff --git a/packages/safe-chain/bin/safe-chain.js b/packages/safe-chain/bin/safe-chain.js
index a89aa6b..5a7d94b 100755
--- a/packages/safe-chain/bin/safe-chain.js
+++ b/packages/safe-chain/bin/safe-chain.js
@@ -4,6 +4,7 @@ import chalk from "chalk";
 import { ui } from "../src/environment/userInteraction.js";
 import { setup } from "../src/shell-integration/setup.js";
 import { teardown } from "../src/shell-integration/teardown.js";
+import { setupCi } from "../src/shell-integration/setup-ci.js";
 
 if (process.argv.length < 3) {
   ui.writeError("No command provided. Please provide a command to execute.");
@@ -23,6 +24,8 @@ if (command === "setup") {
   setup();
 } else if (command === "teardown") {
   teardown();
+} else if (command === "setup-ci") {
+  setupCi();
 } else {
   ui.writeError(`Unknown command: ${command}.`);
   ui.emptyLine();
@@ -53,5 +56,10 @@ function writeHelp() {
       "safe-chain teardown"
     )}: This will remove safe-chain aliases from your shell configuration.`
   );
+  ui.writeInformation(
+    `- ${chalk.cyan(
+      "safe-chain setup-ci"
+    )}: This will setup safe-chain for CI environments by creating shims and modifying the PATH.`
+  );
   ui.emptyLine();
 }
diff --git a/packages/safe-chain/src/shell-integration/helpers.js b/packages/safe-chain/src/shell-integration/helpers.js
index aac54d6..4137471 100644
--- a/packages/safe-chain/src/shell-integration/helpers.js
+++ b/packages/safe-chain/src/shell-integration/helpers.js
@@ -13,6 +13,22 @@ export const knownAikidoTools = [
   // and add the documentation for the new tool in the README.md
 ];
 
+/**
+ * Returns a formatted string listing all supported package managers.
+ * Example: "npm, npx, yarn, pnpm, and pnpx commands"
+ */
+export function getPackageManagerList() {
+  const tools = knownAikidoTools.map(t => t.tool);
+  if (tools.length <= 1) {
+    return `${tools[0] || ''} commands`;
+  }
+  if (tools.length === 2) {
+    return `${tools[0]} and ${tools[1]} commands`;
+  }
+  const lastTool = tools.pop();
+  return `${tools.join(', ')}, and ${lastTool} commands`;
+}
+
 export function doesExecutableExistOnSystem(executableName) {
   if (os.platform() === "win32") {
     const result = spawnSync("where", [executableName], { stdio: "ignore" });
diff --git a/packages/safe-chain/src/shell-integration/path-wrappers/templates/unix-wrapper.template.sh b/packages/safe-chain/src/shell-integration/path-wrappers/templates/unix-wrapper.template.sh
new file mode 100644
index 0000000..6e6d826
--- /dev/null
+++ b/packages/safe-chain/src/shell-integration/path-wrappers/templates/unix-wrapper.template.sh
@@ -0,0 +1,22 @@
+#!/bin/sh
+# Generated wrapper for {{PACKAGE_MANAGER}} by safe-chain
+# This wrapper intercepts {{PACKAGE_MANAGER}} calls for non-interactive environments
+
+# Function to remove shim from PATH (POSIX-compliant)
+remove_shim_from_path() {
+    echo "$PATH" | sed "s|$HOME/.safe-chain/shims:||g"
+}
+
+if command -v {{AIKIDO_COMMAND}} >/dev/null 2>&1; then
+  # Remove shim directory from PATH when calling {{AIKIDO_COMMAND}} to prevent infinite loops
+  PATH=$(remove_shim_from_path) exec {{AIKIDO_COMMAND}} "$@"
+else
+  # Dynamically find original {{PACKAGE_MANAGER}} (excluding this shim directory)
+  original_cmd=$(PATH=$(remove_shim_from_path) command -v {{PACKAGE_MANAGER}})
+  if [ -n "$original_cmd" ]; then
+    exec "$original_cmd" "$@"
+  else
+    echo "Error: Could not find original {{PACKAGE_MANAGER}}" >&2
+    exit 1
+  fi
+fi
\ No newline at end of file
diff --git a/packages/safe-chain/src/shell-integration/path-wrappers/templates/windows-wrapper.template.cmd b/packages/safe-chain/src/shell-integration/path-wrappers/templates/windows-wrapper.template.cmd
new file mode 100644
index 0000000..b7a65fa
--- /dev/null
+++ b/packages/safe-chain/src/shell-integration/path-wrappers/templates/windows-wrapper.template.cmd
@@ -0,0 +1,24 @@
+@echo off
+REM Generated wrapper for {{PACKAGE_MANAGER}} by safe-chain
+REM This wrapper intercepts {{PACKAGE_MANAGER}} calls for non-interactive environments
+
+REM Remove shim directory from PATH to prevent infinite loops
+set "SHIM_DIR=%USERPROFILE%\.safe-chain\shims"
+call set "CLEAN_PATH=%%PATH:%SHIM_DIR%;=%%"
+
+REM Check if aikido command is available with clean PATH
+set "PATH=%CLEAN_PATH%" & where {{AIKIDO_COMMAND}} >nul 2>&1
+if %errorlevel%==0 (
+    REM Call aikido command with clean PATH
+    set "PATH=%CLEAN_PATH%" & {{AIKIDO_COMMAND}} %*
+) else (
+    REM Find the original command with clean PATH
+    for /f "tokens=*" %%i in ('set "PATH=%CLEAN_PATH%" ^& where {{PACKAGE_MANAGER}} 2^>nul') do (
+        "%%i" %*
+        goto :eof
+    )
+    
+    REM If we get here, original command was not found
+    echo Error: Could not find original {{PACKAGE_MANAGER}} >&2
+    exit /b 1
+)
\ No newline at end of file
diff --git a/packages/safe-chain/src/shell-integration/setup-ci.js b/packages/safe-chain/src/shell-integration/setup-ci.js
new file mode 100644
index 0000000..0449ac4
--- /dev/null
+++ b/packages/safe-chain/src/shell-integration/setup-ci.js
@@ -0,0 +1,123 @@
+import chalk from "chalk";
+import { ui } from "../environment/userInteraction.js";
+import { knownAikidoTools, getPackageManagerList } from "./helpers.js";
+import fs from "fs";
+import os from "os";
+import path from "path";
+import { fileURLToPath } from "url";
+
+/**
+ * Loops over the detected shells and calls the setup function for each.
+ */
+export async function setupCi() {
+  ui.writeInformation(
+    chalk.bold("Setting up shell aliases.") +
+      ` This will wrap safe-chain around ${getPackageManagerList()}.`
+  );
+  ui.emptyLine();
+
+  const shimsDir = path.join(os.homedir(), ".safe-chain", "shims");
+  // Create the shims directory if it doesn't exist
+  if (!fs.existsSync(shimsDir)) {
+    fs.mkdirSync(shimsDir, { recursive: true });
+  }
+
+  createShims(shimsDir);
+  ui.writeInformation(`Created shims in ${shimsDir}`);
+  modifyPathForCi(shimsDir);
+  ui.writeInformation(`Added shims directory to PATH for CI environments.`);
+}
+
+function createUnixShims(shimsDir) {
+  // Read the template file
+  const __filename = fileURLToPath(import.meta.url);
+  const __dirname = path.dirname(__filename);
+  const templatePath = path.resolve(
+    __dirname,
+    "path-wrappers",
+    "templates",
+    "unix-wrapper.template.sh"
+  );
+
+  if (!fs.existsSync(templatePath)) {
+    ui.writeError(`Template file not found: ${templatePath}`);
+    return;
+  }
+
+  const template = fs.readFileSync(templatePath, "utf-8");
+
+  // Create a shim for each tool
+  for (const toolInfo of knownAikidoTools) {
+    const shimContent = template
+      .replaceAll("{{PACKAGE_MANAGER}}", toolInfo.tool)
+      .replaceAll("{{AIKIDO_COMMAND}}", toolInfo.aikidoCommand);
+
+    const shimPath = path.join(shimsDir, toolInfo.tool);
+    fs.writeFileSync(shimPath, shimContent, "utf-8");
+
+    // Make the shim executable on Unix systems
+    fs.chmodSync(shimPath, 0o755);
+  }
+
+  ui.writeInformation(
+    `Created ${knownAikidoTools.length} Unix shim(s) in ${shimsDir}`
+  );
+}
+
+function createWindowsShims(shimsDir) {
+  // Read the template file
+  const __filename = fileURLToPath(import.meta.url);
+  const __dirname = path.dirname(__filename);
+  const templatePath = path.resolve(
+    __dirname,
+    "path-wrappers",
+    "templates",
+    "windows-wrapper.template.cmd"
+  );
+
+  if (!fs.existsSync(templatePath)) {
+    ui.writeError(`Windows template file not found: ${templatePath}`);
+    return;
+  }
+
+  const template = fs.readFileSync(templatePath, "utf-8");
+
+  // Create a shim for each tool
+  for (const toolInfo of knownAikidoTools) {
+    const shimContent = template
+      .replaceAll("{{PACKAGE_MANAGER}}", toolInfo.tool)
+      .replaceAll("{{AIKIDO_COMMAND}}", toolInfo.aikidoCommand);
+
+    const shimPath = path.join(shimsDir, `${toolInfo.tool}.cmd`);
+    fs.writeFileSync(shimPath, shimContent, "utf-8");
+  }
+
+  ui.writeInformation(
+    `Created ${knownAikidoTools.length} Windows shim(s) in ${shimsDir}`
+  );
+}
+
+function createShims(shimsDir) {
+  if (os.platform() === "win32") {
+    createWindowsShims(shimsDir);
+  } else {
+    createUnixShims(shimsDir);
+  }
+}
+
+function modifyPathForCi(shimsDir) {
+  if (process.env.GITHUB_PATH) {
+    // In GitHub Actions, append the shims directory to GITHUB_PATH
+    fs.appendFileSync(process.env.GITHUB_PATH, shimsDir + os.EOL, "utf-8");
+    ui.writeInformation(
+      `Added shims directory to GITHUB_PATH for GitHub Actions.`
+    );
+  }
+
+  if (process.env.TF_BUILD) {
+    // In Azure Pipelines, prepending the path is done via a logging command:
+    //  ##vso[task.prependpath]/path/to/add
+    // Logging this to stdout will cause the Azure Pipelines agent to pick it up
+    ui.writeInformation("##vso[task.prependpath]" + shimsDir);
+  }
+}
diff --git a/packages/safe-chain/src/shell-integration/setup-ci.spec.js b/packages/safe-chain/src/shell-integration/setup-ci.spec.js
new file mode 100644
index 0000000..0a26124
--- /dev/null
+++ b/packages/safe-chain/src/shell-integration/setup-ci.spec.js
@@ -0,0 +1,150 @@
+import { describe, it, beforeEach, afterEach, mock } from "node:test";
+import assert from "node:assert";
+import { tmpdir } from "node:os";
+import fs from "node:fs";
+import path from "path";
+
+describe("Setup CI shell integration", () => {
+  let mockShimsDir;
+  let mockTemplateDir;
+  let setupCi;
+  let mockHomeDir;
+  let mockPlatform;
+
+  beforeEach(async () => {
+    mockPlatform = "linux";
+    // Create temporary directories for testing
+    mockHomeDir = path.join(tmpdir(), `test-home-${Date.now()}`);
+    mockShimsDir = path.join(mockHomeDir, ".safe-chain", "shims");
+    mockTemplateDir = path.join(tmpdir(), `test-templates-${Date.now()}`);
+
+    // Create template directories and files
+    fs.mkdirSync(path.join(mockTemplateDir, "path-wrappers", "templates"), { recursive: true });
+    fs.writeFileSync(
+      path.join(mockTemplateDir, "path-wrappers", "templates", "unix-wrapper.template.sh"),
+      "#!/bin/bash\n# Template for {{PACKAGE_MANAGER}}\nexec {{AIKIDO_COMMAND}} \"$@\"\n",
+      "utf-8"
+    );
+    fs.writeFileSync(
+      path.join(mockTemplateDir, "path-wrappers", "templates", "windows-wrapper.template.cmd"),
+      "@echo off\nREM Template for {{PACKAGE_MANAGER}}\n{{AIKIDO_COMMAND}} %*\n",
+      "utf-8"
+    );
+
+    // Mock the ui module
+    mock.module("../environment/userInteraction.js", {
+      namedExports: {
+        ui: {
+          writeInformation: () => {},
+          emptyLine: () => {},
+          writeError: () => {},
+        },
+      },
+    });
+
+    // Mock the helpers module
+    mock.module("./helpers.js", {
+      namedExports: {
+        knownAikidoTools: [
+          { tool: "npm", aikidoCommand: "aikido-npm" },
+          { tool: "yarn", aikidoCommand: "aikido-yarn" },
+        ],
+        getPackageManagerList: () => "npm, yarn",
+      },
+    });
+
+    // Mock os module
+    mock.module("os", {
+      namedExports: {
+        homedir: () => mockHomeDir,
+        platform: () => mockPlatform,
+        EOL: "\n",
+      },
+    });
+
+    // Mock path module to resolve templates correctly
+    mock.module("path", {
+      namedExports: {
+        join: path.join,
+        dirname: () => mockTemplateDir,
+        resolve: (...args) => path.resolve(mockTemplateDir, ...args.slice(1)),
+      },
+    });
+
+    // Mock fileURLToPath
+    mock.module("url", {
+      namedExports: {
+        fileURLToPath: () => path.join(mockTemplateDir, "setup-ci.js"),
+      },
+    });
+
+    // Import setupCi module after mocking
+    setupCi = (await import("./setup-ci.js")).setupCi;
+  });
+
+  afterEach(() => {
+    // Clean up test directories
+    if (fs.existsSync(mockShimsDir)) {
+      fs.rmSync(mockShimsDir, { recursive: true, force: true });
+    }
+    if (fs.existsSync(mockHomeDir)) {
+      fs.rmSync(mockHomeDir, { recursive: true, force: true });
+    }
+    if (fs.existsSync(mockTemplateDir)) {
+      fs.rmSync(mockTemplateDir, { recursive: true, force: true });
+    }
+
+    // Reset mocks
+    mock.reset();
+    mockPlatform = "linux";
+  });
+
+  describe("setupCi", () => {
+    it("should create shims directory and Unix shims", async () => {
+      await setupCi();
+
+      // Check if shims directory was created
+      assert.ok(fs.existsSync(mockShimsDir), "Shims directory should exist");
+
+      // Check if npm shim was created
+      const npmShimPath = path.join(mockShimsDir, "npm");
+      assert.ok(fs.existsSync(npmShimPath), "npm shim should exist");
+
+      // Check if yarn shim was created
+      const yarnShimPath = path.join(mockShimsDir, "yarn");
+      assert.ok(fs.existsSync(yarnShimPath), "yarn shim should exist");
+
+      // Check content of npm shim
+      const npmShimContent = fs.readFileSync(npmShimPath, "utf-8");
+      assert.ok(npmShimContent.includes("aikido-npm"), "npm shim should contain aikido-npm");
+      assert.ok(npmShimContent.includes("#!/bin/bash"), "npm shim should have bash shebang");
+    });
+
+    it("should create Windows .cmd shims on win32 platform", async () => {
+      // Change platform for this test
+      mockPlatform = "win32";
+
+      await setupCi();
+
+      // Check if shims directory was created
+      assert.ok(fs.existsSync(mockShimsDir), "Shims directory should exist");
+
+      // Check if .cmd files were created instead of Unix scripts
+      const npmShimPath = path.join(mockShimsDir, "npm.cmd");
+      assert.ok(fs.existsSync(npmShimPath), "npm.cmd shim should exist");
+
+      const yarnShimPath = path.join(mockShimsDir, "yarn.cmd");
+      assert.ok(fs.existsSync(yarnShimPath), "yarn.cmd shim should exist");
+
+      // Check content of npm.cmd shim
+      const npmShimContent = fs.readFileSync(npmShimPath, "utf-8");
+      assert.ok(npmShimContent.includes("aikido-npm"), "npm.cmd should contain aikido-npm");
+      assert.ok(npmShimContent.includes("@echo off"), "npm.cmd should have Windows batch header");
+      assert.ok(npmShimContent.includes("%*"), "npm.cmd should use Windows argument passing");
+
+      // Verify Unix shims were NOT created
+      const unixNpmShim = path.join(mockShimsDir, "npm");
+      assert.ok(!fs.existsSync(unixNpmShim), "Unix npm shim should not exist on Windows");
+    });
+  });
+});
\ No newline at end of file
diff --git a/packages/safe-chain/src/shell-integration/setup.js b/packages/safe-chain/src/shell-integration/setup.js
index b58eb51..afa96e8 100644
--- a/packages/safe-chain/src/shell-integration/setup.js
+++ b/packages/safe-chain/src/shell-integration/setup.js
@@ -1,7 +1,7 @@
 import chalk from "chalk";
 import { ui } from "../environment/userInteraction.js";
 import { detectShells } from "./shellDetection.js";
-import { knownAikidoTools } from "./helpers.js";
+import { knownAikidoTools, getPackageManagerList } from "./helpers.js";
 import fs from "fs";
 import os from "os";
 import path from "path";
@@ -13,7 +13,7 @@ import { fileURLToPath } from "url";
 export async function setup() {
   ui.writeInformation(
     chalk.bold("Setting up shell aliases.") +
-      " This will wrap safe-chain around npm, npx, and yarn commands."
+      ` This will wrap safe-chain around ${getPackageManagerList()}.`
   );
   ui.emptyLine();
 
diff --git a/packages/safe-chain/src/shell-integration/teardown.js b/packages/safe-chain/src/shell-integration/teardown.js
index 9f74300..d6b1277 100644
--- a/packages/safe-chain/src/shell-integration/teardown.js
+++ b/packages/safe-chain/src/shell-integration/teardown.js
@@ -1,12 +1,12 @@
 import chalk from "chalk";
 import { ui } from "../environment/userInteraction.js";
 import { detectShells } from "./shellDetection.js";
-import { knownAikidoTools } from "./helpers.js";
+import { knownAikidoTools, getPackageManagerList } from "./helpers.js";
 
 export async function teardown() {
   ui.writeInformation(
     chalk.bold("Removing shell aliases.") +
-      " This will remove safe-chain aliases for npm, npx, and yarn commands."
+      ` This will remove safe-chain aliases for ${getPackageManagerList()}.`
   );
   ui.emptyLine();
 
diff --git a/test/e2e/npm-ci.e2e.spec.js b/test/e2e/npm-ci.e2e.spec.js
new file mode 100644
index 0000000..3e08c3d
--- /dev/null
+++ b/test/e2e/npm-ci.e2e.spec.js
@@ -0,0 +1,103 @@
+import { describe, it, before, beforeEach, afterEach } from "node:test";
+import { DockerTestContainer } from "./DockerTestContainer.js";
+import assert from "node:assert";
+
+describe("E2E: npm coverage using PATH", () => {
+  let container;
+
+  before(async () => {
+    DockerTestContainer.buildImage();
+  });
+
+  beforeEach(async () => {
+    // Run a new Docker container for each test
+    container = new DockerTestContainer();
+    await container.start();
+
+    const installationShell = await container.openShell("zsh");
+    await installationShell.runCommand("safe-chain setup-ci");
+
+    // Add $HOME/.safe-chain/shims to PATH for the test commands
+    await installationShell.runCommand(
+      "echo 'export PATH=\"$HOME/.safe-chain/shims:$PATH\"' >> ~/.zshrc"
+    );
+  });
+
+  afterEach(async () => {
+    // Stop and clean up the container after each test
+    if (container) {
+      await container.stop();
+      container = null;
+    }
+  });
+
+  it(`safe-chain succesfully installs safe packages`, async () => {
+    const shell = await container.openShell("zsh");
+    const result = await shell.runCommand("npm i axios");
+
+    assert.ok(
+      result.output.includes("No malicious packages detected."),
+      `Output did not include expected text. Output was:\n${result.output}`
+    );
+  });
+
+  it(`safe-chain blocks installation of malicious packages`, async () => {
+    const shell = await container.openShell("zsh");
+    const result = await shell.runCommand("npm i safe-chain-test");
+
+    assert.ok(
+      result.output.includes("Malicious changes detected:"),
+      `Output did not include expected text. Output was:\n${result.output}`
+    );
+    assert.ok(
+      result.output.includes("- safe-chain-test"),
+      `Output did not include expected text. Output was:\n${result.output}`
+    );
+    assert.ok(
+      result.output.includes("Exiting without installing malicious packages."),
+      `Output did not include expected text. Output was:\n${result.output}`
+    );
+
+    const listResult = await shell.runCommand("npm list");
+    assert.ok(
+      !listResult.output.includes("safe-chain-test"),
+      `Malicious package was installed despite safe-chain protection. Output of 'npm list' was:\n${listResult.output}`
+    );
+  });
+
+  it("safe-chain blocks npx from executing malicious packages", async () => {
+    const shell = await container.openShell("zsh");
+    const result = await shell.runCommand("npx safe-chain-test");
+
+    assert.ok(
+      result.output.includes("Malicious changes detected:"),
+      `Output did not include expected text. Output was:\n${result.output}`
+    );
+    assert.ok(
+      result.output.includes("- safe-chain-test"),
+      `Output did not include expected text. Output was:\n${result.output}`
+    );
+    assert.ok(
+      result.output.includes("Exiting without installing malicious packages."),
+      `Output did not include expected text. Output was:\n${result.output}`
+    );
+  });
+
+  it("safe-chain blocks npm exec from executing malicious packages", async () => {
+    const shell = await container.openShell("zsh");
+    const result = await shell.runCommand("npm exec safe-chain-test");
+
+    assert.ok(
+      result.output.includes("Malicious changes detected:"),
+      `Output did not include expected text. Output was:\n${result.output}`
+    );
+    assert.ok(
+      result.output.includes("- safe-chain-test"),
+      `Output did not include expected text. Output was:\n${result.output}`
+    );
+    assert.ok(
+      result.output.includes("Exiting without installing malicious packages."),
+      `Output did not include expected text. Output was:\n${result.output}`
+    );
+  });
+});
diff --git a/test/e2e/pnpm-ci.e2e.spec.js b/test/e2e/pnpm-ci.e2e.spec.js
new file mode 100644
index 0000000..9a8c6a2
--- /dev/null
+++ b/test/e2e/pnpm-ci.e2e.spec.js
@@ -0,0 +1,123 @@
+import { describe, it, before, beforeEach, afterEach } from "node:test";
+import { DockerTestContainer } from "./DockerTestContainer.js";
+import assert from "node:assert";
+
+describe("E2E: pnpm coverage", () => {
+  let container;
+
+  before(async () => {
+    DockerTestContainer.buildImage();
+  });
+
+  beforeEach(async () => {
+    // Run a new Docker container for each test
+    container = new DockerTestContainer();
+    await container.start();
+
+    const installationShell = await container.openShell("zsh");
+    await installationShell.runCommand("safe-chain setup-ci");
+
+    // Add $HOME/.safe-chain/shims to PATH for the test commands
+    await installationShell.runCommand(
+      "echo 'export PATH=\"$HOME/.safe-chain/shims:$PATH\"' >> ~/.zshrc"
+    );
+  });
+
+  afterEach(async () => {
+    // Stop and clean up the container after each test
+    if (container) {
+      await container.stop();
+      container = null;
+    }
+  });
+
+  it(`safe-chain succesfully installs safe packages`, async () => {
+    const shell = await container.openShell("zsh");
+    const result = await shell.runCommand("pnpm add axios");
+
+    assert.ok(
+      result.output.includes("No malicious packages detected."),
+      `Output did not include expected text. Output was:\n${result.output}`
+    );
+  });
+
+  it(`safe-chain blocks installation of malicious packages`, async () => {
+    const shell = await container.openShell("zsh");
+    const result = await shell.runCommand("pnpm add safe-chain-test");
+
+    assert.ok(
+      result.output.includes("Malicious changes detected:"),
+      `Output did not include expected text. Output was:\n${result.output}`
+    );
+    assert.ok(
+      result.output.includes("- safe-chain-test"),
+      `Output did not include expected text. Output was:\n${result.output}`
+    );
+    assert.ok(
+      result.output.includes("Exiting without installing malicious packages."),
+      `Output did not include expected text. Output was:\n${result.output}`
+    );
+
+    const listResult = await shell.runCommand("pnpm list");
+    assert.ok(
+      !listResult.output.includes("safe-chain-test"),
+      `Malicious package was installed despite safe-chain protection. Output of 'pnpm list' was:\n${listResult.output}`
+    );
+  });
+
+  it("safe-chain blocks pnpx from executing malicious packages", async () => {
+    const shell = await container.openShell("zsh");
+    const result = await shell.runCommand("pnpx safe-chain-test");
+
+    assert.ok(
+      result.output.includes("Malicious changes detected:"),
+      `Output did not include expected text. Output was:\n${result.output}`
+    );
+    assert.ok(
+      result.output.includes("- safe-chain-test"),
+      `Output did not include expected text. Output was:\n${result.output}`
+    );
+    assert.ok(
+      result.output.includes("Exiting without installing malicious packages."),
+      `Output did not include expected text. Output was:\n${result.output}`
+    );
+  });
+
+  it("safe-chain blocks pnpm dlx from executing malicious packages", async () => {
+    const shell = await container.openShell("zsh");
+    const result = await shell.runCommand("pnpm dlx safe-chain-test");
+
+    assert.ok(
+      result.output.includes("Malicious changes detected:"),
+      `Output did not include expected text. Output was:\n${result.output}`
+    );
+    assert.ok(
+      result.output.includes("- safe-chain-test"),
+      `Output did not include expected text. Output was:\n${result.output}`
+    );
+    assert.ok(
+      result.output.includes("Exiting without installing malicious packages."),
+      `Output did not include expected text. Output was:\n${result.output}`
+    );
+  });
+
+  it("safe-chain blocks pnpm --package=name dlx from executing malicious packages", async () => {
+    const shell = await container.openShell("zsh");
+    const result = await shell.runCommand(
+      "pnpm --package=safe-chain-test dlx safe-chain-test"
+    );
+
+    assert.ok(
+      result.output.includes("Malicious changes detected:"),
+      `Output did not include expected text. Output was:\n${result.output}`
+    );
+    assert.ok(
+      result.output.includes("- safe-chain-test"),
+      `Output did not include expected text. Output was:\n${result.output}`
+    );
+    assert.ok(
+      result.output.includes("Exiting without installing malicious packages."),
+      `Output did not include expected text. Output was:\n${result.output}`
+    );
+  });
+});
diff --git a/test/e2e/setup-ci.e2e.spec.js b/test/e2e/setup-ci.e2e.spec.js
new file mode 100644
index 0000000..9356f88
--- /dev/null
+++ b/test/e2e/setup-ci.e2e.spec.js
@@ -0,0 +1,82 @@
+import { describe, it, before, beforeEach, afterEach } from "node:test";
+import { DockerTestContainer } from "./DockerTestContainer.js";
+import assert from "node:assert";
+
+describe("E2E: safe-chain setup-ci command", () => {
+  let container;
+
+  before(async () => {
+    DockerTestContainer.buildImage();
+  });
+
+  beforeEach(async () => {
+    container = new DockerTestContainer();
+    await container.start();
+  });
+
+  afterEach(async () => {
+    if (container) {
+      await container.stop();
+      container = null;
+    }
+  });
+
+  for (let shell of ["bash", "zsh"]) {
+    it(`safe-chain setup-ci wraps npm command with PATH shim after installation for ${shell}`, async () => {
+      // setting up the container
+      const installationShell = await container.openShell(shell);
+      await installationShell.runCommand("safe-chain setup-ci");
+
+      // Add $HOME/.safe-chain/shims to PATH for the test commands
+      // Usually this would be done by adding ENV in a Dockerfile, or by
+      // the CI system picking up GITHUB_PATH or similar. Here we do it manually
+      // to simulate the effect.
+      await installationShell.runCommand(
+        "echo 'export PATH=\"$HOME/.safe-chain/shims:$PATH\"' >> ~/.zshrc"
+      );
+      await installationShell.runCommand(
+        "echo 'export PATH=\"$HOME/.safe-chain/shims:$PATH\"' >> ~/.bashrc"
+      );
+
+      const projectShell = await container.openShell(shell);
+      const result = await projectShell.runCommand("npm i axios");
+
+      const hasExpectedOutput = result.output.includes(
+        "Scanning for malicious packages..."
+      );
+      assert.ok(
+        hasExpectedOutput,
+        hasExpectedOutput
+          ? "Expected npm command to be wrapped by safe-chain"
+          : `Output did not contain "Scanning for malicious packages...": \n${result.output}`
+      );
+    });
+  }
+
+  it("writes to GITHUB_PATH when GITHUB_PATH is set", async () => {
+    const installationShell = await container.openShell("zsh");
+    await installationShell.runCommand("export GITHUB_PATH=/tmp/github_path");
+    await installationShell.runCommand("safe-chain setup-ci");
+
+    const result = await installationShell.runCommand(
+      "cat /tmp/github_path | grep '.safe-chain/shims'"
+    );
+
+    assert.ok(
+      result.output.includes("/root/.safe-chain/shims"),
+      `GITHUB_PATH did not contain expected shim path. Output was:\n${result.output}`
+    );
+  });
+
+  it("writes ##vso[task.prependpath] when TF_BUILD is set", async () => {
+    const installationShell = await container.openShell("zsh");
+    await installationShell.runCommand("export TF_BUILD=true");
+
+    var result = await installationShell.runCommand("safe-chain setup-ci");
+
+    assert.ok(
+      result.output.includes("##vso[task.prependpath]/root/.safe-chain/shims"),
+      `TF_BUILD did not contain expected prepend path. Output was:\n${result.output}`
+    );
+  });
+});
diff --git a/test/e2e/yarn-ci.e2e.spec.js b/test/e2e/yarn-ci.e2e.spec.js
new file mode 100644
index 0000000..5466851
--- /dev/null
+++ b/test/e2e/yarn-ci.e2e.spec.js
@@ -0,0 +1,85 @@
+import { describe, it, before, beforeEach, afterEach } from "node:test";
+import { DockerTestContainer } from "./DockerTestContainer.js";
+import assert from "node:assert";
+
+describe("E2E: yarn coverage", () => {
+  let container;
+
+  before(async () => {
+    DockerTestContainer.buildImage();
+  });
+
+  beforeEach(async () => {
+    // Run a new Docker container for each test
+    container = new DockerTestContainer();
+    await container.start();
+
+    const installationShell = await container.openShell("zsh");
+    await installationShell.runCommand("safe-chain setup-ci");
+
+    // Add $HOME/.safe-chain/shims to PATH for the test commands
+    await installationShell.runCommand(
+      "echo 'export PATH=\"$HOME/.safe-chain/shims:$PATH\"' >> ~/.zshrc"
+    );
+  });
+
+  afterEach(async () => {
+    // Stop and clean up the container after each test
+    if (container) {
+      await container.stop();
+      container = null;
+    }
+  });
+
+  it(`safe-chain succesfully installs safe packages`, async () => {
+    const shell = await container.openShell("zsh");
+    const result = await shell.runCommand("yarn add axios");
+
+    assert.ok(
+      result.output.includes("No malicious packages detected."),
+      `Output did not include expected text. Output was:\n${result.output}`
+    );
+  });
+
+  it(`safe-chain blocks installation of malicious packages`, async () => {
+    const shell = await container.openShell("zsh");
+    const result = await shell.runCommand("yarn add safe-chain-test");
+
+    assert.ok(
+      result.output.includes("Malicious changes detected:"),
+      `Output did not include expected text. Output was:\n${result.output}`
+    );
+    assert.ok(
+      result.output.includes("- safe-chain-test"),
+      `Output did not include expected text. Output was:\n${result.output}`
+    );
+    assert.ok(
+      result.output.includes("Exiting without installing malicious packages."),
+      `Output did not include expected text. Output was:\n${result.output}`
+    );
+
+    const listResult = await shell.runCommand("yarn list");
+    assert.ok(
+      !listResult.output.includes("safe-chain-test"),
+      `Malicious package was installed despite safe-chain protection. Output of 'yarn list' was:\n${listResult.output}`
+    );
+  });
+
+  it("safe-chain blocks yarn dlx from executing malicious packages", async () => {
+    const shell = await container.openShell("zsh");
+    const result = await shell.runCommand("yarn dlx safe-chain-test");
+
+    assert.ok(
+      result.output.includes("Malicious changes detected:"),
+      `Output did not include expected text. Output was:\n${result.output}`
+    );
+    assert.ok(
+      result.output.includes("- safe-chain-test"),
+      `Output did not include expected text. Output was:\n${result.output}`
+    );
+    assert.ok(
+      result.output.includes("Exiting without installing malicious packages."),
+      `Output did not include expected text. Output was:\n${result.output}`
+    );
+  });
+});