diff --git a/packages/safe-chain/bin/safe-chain.js b/packages/safe-chain/bin/safe-chain.js
index 2793987..802005b 100755
--- a/packages/safe-chain/bin/safe-chain.js
+++ b/packages/safe-chain/bin/safe-chain.js
@@ -3,7 +3,7 @@
 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 { teardown, teardownDirectories } from "../src/shell-integration/teardown.js";
 import { setupCi } from "../src/shell-integration/setup-ci.js";
 import { initializeCliArguments } from "../src/config/cliArguments.js";
 import { setEcoSystem } from "../src/config/settings.js";
@@ -60,6 +60,7 @@ if (tool) {
 } else if (command === "setup") {
   setup();
 } else if (command === "teardown") {
+  teardownDirectories();
   teardown();
 } else if (command === "setup-ci") {
   setupCi();
diff --git a/packages/safe-chain/src/shell-integration/helpers.js b/packages/safe-chain/src/shell-integration/helpers.js
index 50cea5d..3b08bf2 100644
--- a/packages/safe-chain/src/shell-integration/helpers.js
+++ b/packages/safe-chain/src/shell-integration/helpers.js
@@ -113,6 +113,20 @@ export function getPackageManagerList() {
   return `${tools.join(", ")}, and ${lastTool} commands`;
 }
 
+/**
+ * @returns {string}
+ */
+export function getShimsDir() {
+  return path.join(os.homedir(), ".safe-chain", "shims");
+}
+
+/**
+ * @returns {string}
+ */
+export function getScriptsDir() {
+  return path.join(os.homedir(), ".safe-chain", "scripts");
+}
+
 /**
  * @param {string} executableName
  *
diff --git a/packages/safe-chain/src/shell-integration/setup-ci.js b/packages/safe-chain/src/shell-integration/setup-ci.js
index bc5c5e6..b0a8c83 100644
--- a/packages/safe-chain/src/shell-integration/setup-ci.js
+++ b/packages/safe-chain/src/shell-integration/setup-ci.js
@@ -1,6 +1,6 @@
 import chalk from "chalk";
 import { ui } from "../environment/userInteraction.js";
-import { getPackageManagerList, knownAikidoTools } from "./helpers.js";
+import { getPackageManagerList, knownAikidoTools, getShimsDir } from "./helpers.js";
 import fs from "fs";
 import os from "os";
 import path from "path";
@@ -32,7 +32,7 @@ export async function setupCi() {
   );
   ui.emptyLine();
 
-  const shimsDir = path.join(os.homedir(), ".safe-chain", "shims");
+  const shimsDir = getShimsDir();
   const binDir = path.join(os.homedir(), ".safe-chain", "bin");
   // Create the shims directory if it doesn't exist
   if (!fs.existsSync(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
index 92ef82e..b437157 100644
--- a/packages/safe-chain/src/shell-integration/setup-ci.spec.js
+++ b/packages/safe-chain/src/shell-integration/setup-ci.spec.js
@@ -50,6 +50,7 @@ describe("Setup CI shell integration", () => {
           { tool: "yarn", aikidoCommand: "aikido-yarn" },
         ],
         getPackageManagerList: () => "npm, yarn",
+        getShimsDir: () => mockShimsDir,
       },
     });
 
diff --git a/packages/safe-chain/src/shell-integration/setup.js b/packages/safe-chain/src/shell-integration/setup.js
index d5c4be9..065de75 100644
--- a/packages/safe-chain/src/shell-integration/setup.js
+++ b/packages/safe-chain/src/shell-integration/setup.js
@@ -1,9 +1,8 @@
 import chalk from "chalk";
 import { ui } from "../environment/userInteraction.js";
 import { detectShells } from "./shellDetection.js";
-import { knownAikidoTools, getPackageManagerList } from "./helpers.js";
+import { knownAikidoTools, getPackageManagerList, getScriptsDir } from "./helpers.js";
 import fs from "fs";
-import os from "os";
 import path from "path";
 import { includePython } from "../config/cliArguments.js";
 import { fileURLToPath } from "url";
@@ -107,10 +106,10 @@ function setupShell(shell) {
 
 function copyStartupFiles() {
   const startupFiles = ["init-posix.sh", "init-pwsh.ps1", "init-fish.fish"];
+  const targetDir = getScriptsDir();
 
   for (const file of startupFiles) {
-    const targetDir = path.join(os.homedir(), ".safe-chain", "scripts");
-    const targetPath = path.join(os.homedir(), ".safe-chain", "scripts", file);
+    const targetPath = path.join(targetDir, file);
 
     if (!fs.existsSync(targetDir)) {
       fs.mkdirSync(targetDir, { recursive: true });
diff --git a/packages/safe-chain/src/shell-integration/teardown.js b/packages/safe-chain/src/shell-integration/teardown.js
index bc83b48..de3fbd7 100644
--- a/packages/safe-chain/src/shell-integration/teardown.js
+++ b/packages/safe-chain/src/shell-integration/teardown.js
@@ -1,7 +1,8 @@
 import chalk from "chalk";
 import { ui } from "../environment/userInteraction.js";
 import { detectShells } from "./shellDetection.js";
-import { knownAikidoTools, getPackageManagerList } from "./helpers.js";
+import { knownAikidoTools, getPackageManagerList, getShimsDir, getScriptsDir } from "./helpers.js";
+import fs from "fs";
 
 /**
  * @returns {Promise<void>}
@@ -62,3 +63,44 @@ export async function teardown() {
     return;
   }
 }
+
+/**
+ * Removes directories created by setup-ci and setup commands
+ * @returns {Promise<void>}
+ */
+export async function teardownDirectories() {
+  const shimsDir = getShimsDir();
+  const scriptsDir = getScriptsDir();
+
+  // Remove CI shims directory
+  if (fs.existsSync(shimsDir)) {
+    try {
+      fs.rmSync(shimsDir, { recursive: true, force: true });
+      ui.writeInformation(
+        `${chalk.bold("- CI Shims:")} ${chalk.green("Removed successfully")}`
+      );
+    } catch (/** @type {any} */ error) {
+      ui.writeError(
+        `${chalk.bold("- CI Shims:")} ${chalk.red(
+          "Failed to remove"
+        )}. Error: ${error.message}`
+      );
+    }
+  }
+
+  // Remove scripts directory
+  if (fs.existsSync(scriptsDir)) {
+    try {
+      fs.rmSync(scriptsDir, { recursive: true, force: true });
+      ui.writeInformation(
+        `${chalk.bold("- Scripts:")} ${chalk.green("Removed successfully")}`
+      );
+    } catch (/** @type {any} */ error) {
+      ui.writeError(
+        `${chalk.bold("- Scripts:")} ${chalk.red(
+          "Failed to remove"
+        )}. Error: ${error.message}`
+      );
+    }
+  }
+}
diff --git a/test/e2e/teardown-dirs.e2e.spec.js b/test/e2e/teardown-dirs.e2e.spec.js
new file mode 100644
index 0000000..0ed8bf6
--- /dev/null
+++ b/test/e2e/teardown-dirs.e2e.spec.js
@@ -0,0 +1,99 @@
+import { describe, it, before, beforeEach, afterEach } from "node:test";
+import { DockerTestContainer } from "./DockerTestContainer.js";
+import assert from "node:assert";
+
+describe("E2E: safe-chain teardown command", () => {
+  let container;
+
+  before(async () => {
+    DockerTestContainer.buildImage();
+  });
+
+  beforeEach(async () => {
+    container = new DockerTestContainer();
+    await container.start();
+  });
+
+  afterEach(async () => {
+    if (container) {
+      await container.stop();
+      container = null;
+    }
+  });
+
+  it("safe-chain teardown removes shims directory created by setup-ci", async () => {
+    const shell = await container.openShell("bash");
+
+    // Run setup-ci
+    await shell.runCommand("safe-chain setup-ci");
+
+    // Verify shims directory exists
+    const checkShimsExist = await shell.runCommand("test -d ~/.safe-chain/shims && echo 'exists' || echo 'missing'");
+    assert.ok(checkShimsExist.output.includes("exists"), "Shims directory should exist after setup-ci");
+
+    // Run teardown
+    await shell.runCommand("safe-chain teardown");
+
+    // Verify shims directory is gone
+    const checkShimsGone = await shell.runCommand("test -d ~/.safe-chain/shims && echo 'exists' || echo 'missing'");
+    assert.ok(checkShimsGone.output.includes("missing"), "Shims directory should be removed after teardown");
+  });
+
+  it("safe-chain teardown removes scripts directory created by setup", async () => {
+    const shell = await container.openShell("bash");
+
+    // Run setup
+    await shell.runCommand("safe-chain setup");
+
+    // Verify scripts directory exists
+    const checkScriptsExist = await shell.runCommand("test -d ~/.safe-chain/scripts && echo 'exists' || echo 'missing'");
+    assert.ok(checkScriptsExist.output.includes("exists"), "Scripts directory should exist after setup");
+
+    // Run teardown
+    await shell.runCommand("safe-chain teardown");
+
+    // Verify scripts directory is gone
+    const checkScriptsGone = await shell.runCommand("test -d ~/.safe-chain/scripts && echo 'exists' || echo 'missing'");
+    assert.ok(checkScriptsGone.output.includes("missing"), "Scripts directory should be removed after teardown");
+  });
+
+  it("safe-chain teardown removes shims directory created by setup-ci --include-python", async () => {
+    const shell = await container.openShell("bash");
+
+    // Run setup-ci with --include-python
+    await shell.runCommand("safe-chain setup-ci --include-python");
+
+    // Verify shims directory exists
+    const checkShimsExist = await shell.runCommand("test -d ~/.safe-chain/shims && echo 'exists' || echo 'missing'");
+    assert.ok(checkShimsExist.output.includes("exists"), "Shims directory should exist after setup-ci --include-python");
+
+    // Verify Python shims were created
+    const checkPythonShims = await shell.runCommand("test -f ~/.safe-chain/shims/pip && echo 'exists' || echo 'missing'");
+    assert.ok(checkPythonShims.output.includes("exists"), "Python shims should exist after setup-ci --include-python");
+
+    // Run teardown
+    await shell.runCommand("safe-chain teardown");
+
+    // Verify shims directory is gone
+    const checkShimsGone = await shell.runCommand("test -d ~/.safe-chain/shims && echo 'exists' || echo 'missing'");
+    assert.ok(checkShimsGone.output.includes("missing"), "Shims directory should be removed after teardown");
+  });
+
+  it("safe-chain teardown removes scripts directory created by setup --include-python", async () => {
+    const shell = await container.openShell("bash");
+
+    // Run setup with --include-python
+    await shell.runCommand("safe-chain setup --include-python");
+
+    // Verify scripts directory exists
+    const checkScriptsExist = await shell.runCommand("test -d ~/.safe-chain/scripts && echo 'exists' || echo 'missing'");
+    assert.ok(checkScriptsExist.output.includes("exists"), "Scripts directory should exist after setup --include-python");
+
+    // Run teardown
+    await shell.runCommand("safe-chain teardown");
+
+    // Verify scripts directory is gone
+    const checkScriptsGone = await shell.runCommand("test -d ~/.safe-chain/scripts && echo 'exists' || echo 'missing'");
+    assert.ok(checkScriptsGone.output.includes("missing"), "Scripts directory should be removed after teardown");
+  });
+});