diff --git a/packages/safe-chain/src/registryProxy/certUtils.js b/packages/safe-chain/src/registryProxy/certUtils.js
index 3c8790c..a4bc0b1 100644
--- a/packages/safe-chain/src/registryProxy/certUtils.js
+++ b/packages/safe-chain/src/registryProxy/certUtils.js
@@ -2,12 +2,17 @@ import forge from "node-forge";
 import path from "path";
 import fs from "fs";
 import os from "os";
+import { getSafeChainDir } from "../config/environmentVariables.js";
 
-const certFolder = path.join(os.homedir(), ".safe-chain", "certs");
 const ca = loadCa();
 
 const certCache = new Map();
 
+function getCertFolder() {
+  const safeChainDir = getSafeChainDir() ?? path.join(os.homedir(), ".safe-chain");
+  return path.join(safeChainDir, "certs");
+}
+
 /**
  * @param {forge.pki.PublicKey} publicKey
  * @returns {string}
@@ -20,7 +25,7 @@ function createKeyIdentifier(publicKey) {
 }
 
 export function getCaCertPath() {
-  return path.join(certFolder, "ca-cert.pem");
+  return path.join(getCertFolder(), "ca-cert.pem");
 }
 
 /**
@@ -112,6 +117,7 @@ export function generateCertForHost(hostname) {
 }
 
 function loadCa() {
+  const certFolder = getCertFolder();
   const keyPath = path.join(certFolder, "ca-key.pem");
   const certPath = path.join(certFolder, "ca-cert.pem");
 
diff --git a/packages/safe-chain/src/registryProxy/certUtils.spec.js b/packages/safe-chain/src/registryProxy/certUtils.spec.js
new file mode 100644
index 0000000..ebf8dab
--- /dev/null
+++ b/packages/safe-chain/src/registryProxy/certUtils.spec.js
@@ -0,0 +1,71 @@
+import { describe, it, beforeEach, afterEach, mock } from "node:test";
+import assert from "node:assert";
+
+describe("certUtils", () => {
+  let originalSafeChainDir;
+
+  beforeEach(() => {
+    originalSafeChainDir = process.env.SAFE_CHAIN_DIR;
+  });
+
+  afterEach(() => {
+    if (originalSafeChainDir === undefined) {
+      delete process.env.SAFE_CHAIN_DIR;
+    } else {
+      process.env.SAFE_CHAIN_DIR = originalSafeChainDir;
+    }
+
+    mock.reset();
+  });
+
+  it("stores CA certificates in SAFE_CHAIN_DIR when configured", async () => {
+    process.env.SAFE_CHAIN_DIR = "/custom/safe-chain";
+
+    mock.module("fs", {
+      defaultExport: {
+        existsSync: () => false,
+        mkdirSync: () => {},
+        writeFileSync: () => {},
+      },
+    });
+
+    mock.module("node-forge", {
+      defaultExport: {
+        pki: {
+          getPublicKeyFingerprint: () => "fingerprint",
+          rsa: {
+            generateKeyPair: () => ({
+              publicKey: "public-key",
+              privateKey: "private-key",
+            }),
+          },
+          createCertificate: () => ({
+            publicKey: null,
+            serialNumber: "",
+            validity: {
+              notBefore: new Date(),
+              notAfter: new Date(),
+            },
+            setSubject: () => {},
+            setIssuer: () => {},
+            setExtensions: () => {},
+            sign: () => {},
+          }),
+          privateKeyToPem: () => "private-key-pem",
+          certificateToPem: () => "certificate-pem",
+        },
+        md: {
+          sha1: { create: () => "sha1" },
+          sha256: { create: () => "sha256" },
+        },
+      },
+    });
+
+    const { getCaCertPath } = await import("./certUtils.js");
+
+    assert.strictEqual(
+      getCaCertPath(),
+      "/custom/safe-chain/certs/ca-cert.pem",
+    );
+  });
+});
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
index 082d553..959b700 100644
--- 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
@@ -3,7 +3,11 @@ 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"
+if defined SAFE_CHAIN_DIR (
+    set "SHIM_DIR=%SAFE_CHAIN_DIR%\shims"
+) else (
+    set "SHIM_DIR=%USERPROFILE%\.safe-chain\shims"
+)
 call set "CLEAN_PATH=%%PATH:%SHIM_DIR%;=%%"
 
 REM Check if aikido command is available with clean PATH
@@ -21,4 +25,4 @@ if %errorlevel%==0 (
     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.spec.js b/packages/safe-chain/src/shell-integration/setup-ci.spec.js
index c0a5ca1..1156173 100644
--- a/packages/safe-chain/src/shell-integration/setup-ci.spec.js
+++ b/packages/safe-chain/src/shell-integration/setup-ci.spec.js
@@ -27,7 +27,7 @@ describe("Setup CI shell integration", () => {
     );
     fs.writeFileSync(
       path.join(mockTemplateDir, "path-wrappers", "templates", "windows-wrapper.template.cmd"),
-      "@echo off\nREM Template for {{PACKAGE_MANAGER}}\n{{AIKIDO_COMMAND}} %*\n",
+      "@echo off\nif defined SAFE_CHAIN_DIR (\n    set \"SHIM_DIR=%SAFE_CHAIN_DIR%\\shims\"\n) else (\n    set \"SHIM_DIR=%USERPROFILE%\\.safe-chain\\shims\"\n)\n{{AIKIDO_COMMAND}} %*\n",
       "utf-8"
     );
 
@@ -143,6 +143,10 @@ describe("Setup CI shell integration", () => {
       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");
+      assert.ok(
+        npmShimContent.includes("if defined SAFE_CHAIN_DIR"),
+        "npm.cmd should honor SAFE_CHAIN_DIR when removing shim dir from PATH",
+      );
 
       // Verify Unix shims were NOT created
       const unixNpmShim = path.join(mockShimsDir, "npm");
diff --git a/packages/safe-chain/src/shell-integration/supported-shells/bash.js b/packages/safe-chain/src/shell-integration/supported-shells/bash.js
index 4f04c5e..bcf0bc6 100644
--- a/packages/safe-chain/src/shell-integration/supported-shells/bash.js
+++ b/packages/safe-chain/src/shell-integration/supported-shells/bash.js
@@ -142,19 +142,37 @@ function cygpathw(path) {
 }
 
 function getManualTeardownInstructions() {
-  return [
-    `Remove the following line from your ~/.bashrc file:`,
-    `  source ~/.safe-chain/scripts/init-posix.sh`,
-    `Then restart your terminal or run: source ~/.bashrc`,
-  ];
+  const customDir = getSafeChainDir();
+  const instructions = [`Remove the following line from your ~/.bashrc file:`];
+
+  if (customDir) {
+    instructions.push(
+      `  export SAFE_CHAIN_DIR="${customDir}"`,
+      `  source ${path.join(getScriptsDir(), "init-posix.sh")}`,
+    );
+  } else {
+    instructions.push(`  source ~/.safe-chain/scripts/init-posix.sh`);
+  }
+
+  instructions.push(`Then restart your terminal or run: source ~/.bashrc`);
+  return instructions;
 }
 
 function getManualSetupInstructions() {
-  return [
-    `Add the following line to your ~/.bashrc file:`,
-    `  source ~/.safe-chain/scripts/init-posix.sh`,
-    `Then restart your terminal or run: source ~/.bashrc`,
-  ];
+  const customDir = getSafeChainDir();
+  const instructions = [`Add the following line to your ~/.bashrc file:`];
+
+  if (customDir) {
+    instructions.push(
+      `  export SAFE_CHAIN_DIR="${customDir}"`,
+      `  source ${path.join(getScriptsDir(), "init-posix.sh")}`,
+    );
+  } else {
+    instructions.push(`  source ~/.safe-chain/scripts/init-posix.sh`);
+  }
+
+  instructions.push(`Then restart your terminal or run: source ~/.bashrc`);
+  return instructions;
 }
 
 /**
diff --git a/packages/safe-chain/src/shell-integration/supported-shells/bash.spec.js b/packages/safe-chain/src/shell-integration/supported-shells/bash.spec.js
index a8cd067..4b25d4b 100644
--- a/packages/safe-chain/src/shell-integration/supported-shells/bash.spec.js
+++ b/packages/safe-chain/src/shell-integration/supported-shells/bash.spec.js
@@ -235,6 +235,17 @@ describe("Bash shell integration", () => {
       const content = fs.readFileSync(mockStartupFile, "utf-8");
       assert.ok(!content.includes("SAFE_CHAIN_DIR"));
     });
+
+    it("should show custom manual setup instructions when custom dir is set", () => {
+      getSafeChainDirResult = "/custom/safe-chain";
+
+      assert.deepStrictEqual(bash.getManualSetupInstructions(), [
+        "Add the following line to your ~/.bashrc file:",
+        '  export SAFE_CHAIN_DIR="/custom/safe-chain"',
+        "  source /test-home/.safe-chain/scripts/init-posix.sh",
+        "Then restart your terminal or run: source ~/.bashrc",
+      ]);
+    });
   });
 
   describe("integration tests", () => {
diff --git a/packages/safe-chain/src/shell-integration/supported-shells/fish.js b/packages/safe-chain/src/shell-integration/supported-shells/fish.js
index bac8e7b..33aa48c 100644
--- a/packages/safe-chain/src/shell-integration/supported-shells/fish.js
+++ b/packages/safe-chain/src/shell-integration/supported-shells/fish.js
@@ -85,19 +85,45 @@ function getStartupFile() {
 }
 
 function getManualTeardownInstructions() {
-  return [
+  const customDir = getSafeChainDir();
+  const instructions = [
     `Remove the following line from your ~/.config/fish/config.fish file:`,
-    `  source ~/.safe-chain/scripts/init-fish.fish`,
-    `Then restart your terminal or run: source ~/.config/fish/config.fish`,
   ];
+
+  if (customDir) {
+    instructions.push(
+      `  set -gx SAFE_CHAIN_DIR "${customDir}"`,
+      `  source ${path.join(getScriptsDir(), "init-fish.fish")}`,
+    );
+  } else {
+    instructions.push(`  source ~/.safe-chain/scripts/init-fish.fish`);
+  }
+
+  instructions.push(
+    `Then restart your terminal or run: source ~/.config/fish/config.fish`,
+  );
+  return instructions;
 }
 
 function getManualSetupInstructions() {
-  return [
+  const customDir = getSafeChainDir();
+  const instructions = [
     `Add the following line to your ~/.config/fish/config.fish file:`,
-    `  source ~/.safe-chain/scripts/init-fish.fish`,
-    `Then restart your terminal or run: source ~/.config/fish/config.fish`,
   ];
+
+  if (customDir) {
+    instructions.push(
+      `  set -gx SAFE_CHAIN_DIR "${customDir}"`,
+      `  source ${path.join(getScriptsDir(), "init-fish.fish")}`,
+    );
+  } else {
+    instructions.push(`  source ~/.safe-chain/scripts/init-fish.fish`);
+  }
+
+  instructions.push(
+    `Then restart your terminal or run: source ~/.config/fish/config.fish`,
+  );
+  return instructions;
 }
 
 /**
diff --git a/packages/safe-chain/src/shell-integration/supported-shells/fish.spec.js b/packages/safe-chain/src/shell-integration/supported-shells/fish.spec.js
index c9918c5..29b6d6e 100644
--- a/packages/safe-chain/src/shell-integration/supported-shells/fish.spec.js
+++ b/packages/safe-chain/src/shell-integration/supported-shells/fish.spec.js
@@ -187,6 +187,17 @@ describe("Fish shell integration", () => {
       const content = fs.readFileSync(mockStartupFile, "utf-8");
       assert.ok(!content.includes("SAFE_CHAIN_DIR"));
     });
+
+    it("should show custom manual setup instructions when custom dir is set", () => {
+      getSafeChainDirResult = "/custom/safe-chain";
+
+      assert.deepStrictEqual(fish.getManualSetupInstructions(), [
+        "Add the following line to your ~/.config/fish/config.fish file:",
+        '  set -gx SAFE_CHAIN_DIR "/custom/safe-chain"',
+        "  source /test-home/.safe-chain/scripts/init-fish.fish",
+        "Then restart your terminal or run: source ~/.config/fish/config.fish",
+      ]);
+    });
   });
 
   describe("integration tests", () => {
diff --git a/packages/safe-chain/src/shell-integration/supported-shells/powershell.js b/packages/safe-chain/src/shell-integration/supported-shells/powershell.js
index 38b0b42..44fbfe9 100644
--- a/packages/safe-chain/src/shell-integration/supported-shells/powershell.js
+++ b/packages/safe-chain/src/shell-integration/supported-shells/powershell.js
@@ -88,19 +88,41 @@ function getStartupFile() {
 }
 
 function getManualTeardownInstructions() {
-  return [
+  const customDir = getSafeChainDir();
+  const instructions = [
     `Remove the following line from your PowerShell profile (run "echo $PROFILE" to find its location):`,
-    `  . "$HOME\\.safe-chain\\scripts\\init-pwsh.ps1"`,
-    `Then restart your terminal or run: . $PROFILE`,
   ];
+
+  if (customDir) {
+    instructions.push(
+      `  $env:SAFE_CHAIN_DIR = '${customDir}'`,
+      `  . "${path.join(getScriptsDir(), "init-pwsh.ps1")}"`,
+    );
+  } else {
+    instructions.push(`  . "$HOME\\.safe-chain\\scripts\\init-pwsh.ps1"`);
+  }
+
+  instructions.push(`Then restart your terminal or run: . $PROFILE`);
+  return instructions;
 }
 
 function getManualSetupInstructions() {
-  return [
+  const customDir = getSafeChainDir();
+  const instructions = [
     `Add the following line to your PowerShell profile (run "echo $PROFILE" to find its location):`,
-    `  . "$HOME\\.safe-chain\\scripts\\init-pwsh.ps1"`,
-    `Then restart your terminal or run: . $PROFILE`,
   ];
+
+  if (customDir) {
+    instructions.push(
+      `  $env:SAFE_CHAIN_DIR = '${customDir}'`,
+      `  . "${path.join(getScriptsDir(), "init-pwsh.ps1")}"`,
+    );
+  } else {
+    instructions.push(`  . "$HOME\\.safe-chain\\scripts\\init-pwsh.ps1"`);
+  }
+
+  instructions.push(`Then restart your terminal or run: . $PROFILE`);
+  return instructions;
 }
 
 /**
diff --git a/packages/safe-chain/src/shell-integration/supported-shells/powershell.spec.js b/packages/safe-chain/src/shell-integration/supported-shells/powershell.spec.js
index 97901f1..296abfa 100644
--- a/packages/safe-chain/src/shell-integration/supported-shells/powershell.spec.js
+++ b/packages/safe-chain/src/shell-integration/supported-shells/powershell.spec.js
@@ -241,6 +241,17 @@ describe("PowerShell Core shell integration", () => {
       const content = fs.readFileSync(mockStartupFile, "utf-8");
       assert.ok(!content.includes("SAFE_CHAIN_DIR"));
     });
+
+    it("should show custom manual setup instructions when custom dir is set", () => {
+      getSafeChainDirResult = "C:\\custom\\safe-chain";
+
+      assert.deepStrictEqual(powershell.getManualSetupInstructions(), [
+        'Add the following line to your PowerShell profile (run "echo $PROFILE" to find its location):',
+        "  $env:SAFE_CHAIN_DIR = 'C:\\custom\\safe-chain'",
+        '  . "/test-home/.safe-chain/scripts/init-pwsh.ps1"',
+        "Then restart your terminal or run: . $PROFILE",
+      ]);
+    });
   });
 
   describe("execution policy", () => {
diff --git a/packages/safe-chain/src/shell-integration/supported-shells/windowsPowershell.js b/packages/safe-chain/src/shell-integration/supported-shells/windowsPowershell.js
index 506b891..e3ed236 100644
--- a/packages/safe-chain/src/shell-integration/supported-shells/windowsPowershell.js
+++ b/packages/safe-chain/src/shell-integration/supported-shells/windowsPowershell.js
@@ -88,19 +88,41 @@ function getStartupFile() {
 }
 
 function getManualTeardownInstructions() {
-  return [
+  const customDir = getSafeChainDir();
+  const instructions = [
     `Remove the following line from your PowerShell profile (run "echo $PROFILE" to find its location):`,
-    `  . "$HOME\\.safe-chain\\scripts\\init-pwsh.ps1"`,
-    `Then restart your terminal or run: . $PROFILE`,
   ];
+
+  if (customDir) {
+    instructions.push(
+      `  $env:SAFE_CHAIN_DIR = '${customDir}'`,
+      `  . "${path.join(getScriptsDir(), "init-pwsh.ps1")}"`,
+    );
+  } else {
+    instructions.push(`  . "$HOME\\.safe-chain\\scripts\\init-pwsh.ps1"`);
+  }
+
+  instructions.push(`Then restart your terminal or run: . $PROFILE`);
+  return instructions;
 }
 
 function getManualSetupInstructions() {
-  return [
+  const customDir = getSafeChainDir();
+  const instructions = [
     `Add the following line to your PowerShell profile (run "echo $PROFILE" to find its location):`,
-    `  . "$HOME\\.safe-chain\\scripts\\init-pwsh.ps1"`,
-    `Then restart your terminal or run: . $PROFILE`,
   ];
+
+  if (customDir) {
+    instructions.push(
+      `  $env:SAFE_CHAIN_DIR = '${customDir}'`,
+      `  . "${path.join(getScriptsDir(), "init-pwsh.ps1")}"`,
+    );
+  } else {
+    instructions.push(`  . "$HOME\\.safe-chain\\scripts\\init-pwsh.ps1"`);
+  }
+
+  instructions.push(`Then restart your terminal or run: . $PROFILE`);
+  return instructions;
 }
 
 /**
diff --git a/packages/safe-chain/src/shell-integration/supported-shells/windowsPowershell.spec.js b/packages/safe-chain/src/shell-integration/supported-shells/windowsPowershell.spec.js
index efb5cc3..840f585 100644
--- a/packages/safe-chain/src/shell-integration/supported-shells/windowsPowershell.spec.js
+++ b/packages/safe-chain/src/shell-integration/supported-shells/windowsPowershell.spec.js
@@ -241,6 +241,17 @@ describe("Windows PowerShell shell integration", () => {
       const content = fs.readFileSync(mockStartupFile, "utf-8");
       assert.ok(!content.includes("SAFE_CHAIN_DIR"));
     });
+
+    it("should show custom manual teardown instructions when custom dir is set", () => {
+      getSafeChainDirResult = "C:\\custom\\safe-chain";
+
+      assert.deepStrictEqual(windowsPowershell.getManualTeardownInstructions(), [
+        'Remove the following line from your PowerShell profile (run "echo $PROFILE" to find its location):',
+        "  $env:SAFE_CHAIN_DIR = 'C:\\custom\\safe-chain'",
+        '  . "/test-home/.safe-chain/scripts/init-pwsh.ps1"',
+        "Then restart your terminal or run: . $PROFILE",
+      ]);
+    });
   });
 
   describe("execution policy", () => {
diff --git a/packages/safe-chain/src/shell-integration/supported-shells/zsh.js b/packages/safe-chain/src/shell-integration/supported-shells/zsh.js
index a340424..b2c29e4 100644
--- a/packages/safe-chain/src/shell-integration/supported-shells/zsh.js
+++ b/packages/safe-chain/src/shell-integration/supported-shells/zsh.js
@@ -85,19 +85,37 @@ function getStartupFile() {
 }
 
 function getManualTeardownInstructions() {
-  return [
-    `Remove the following line from your ~/.zshrc file:`,
-    `  source ~/.safe-chain/scripts/init-posix.sh`,
-    `Then restart your terminal or run: source ~/.zshrc`,
-  ];
+  const customDir = getSafeChainDir();
+  const instructions = [`Remove the following line from your ~/.zshrc file:`];
+
+  if (customDir) {
+    instructions.push(
+      `  export SAFE_CHAIN_DIR="${customDir}"`,
+      `  source ${path.join(getScriptsDir(), "init-posix.sh")}`,
+    );
+  } else {
+    instructions.push(`  source ~/.safe-chain/scripts/init-posix.sh`);
+  }
+
+  instructions.push(`Then restart your terminal or run: source ~/.zshrc`);
+  return instructions;
 }
 
 function getManualSetupInstructions() {
-  return [
-    `Add the following line to your ~/.zshrc file:`,
-    `  source ~/.safe-chain/scripts/init-posix.sh`,
-    `Then restart your terminal or run: source ~/.zshrc`,
-  ];
+  const customDir = getSafeChainDir();
+  const instructions = [`Add the following line to your ~/.zshrc file:`];
+
+  if (customDir) {
+    instructions.push(
+      `  export SAFE_CHAIN_DIR="${customDir}"`,
+      `  source ${path.join(getScriptsDir(), "init-posix.sh")}`,
+    );
+  } else {
+    instructions.push(`  source ~/.safe-chain/scripts/init-posix.sh`);
+  }
+
+  instructions.push(`Then restart your terminal or run: source ~/.zshrc`);
+  return instructions;
 }
 
 export default {
diff --git a/packages/safe-chain/src/shell-integration/supported-shells/zsh.spec.js b/packages/safe-chain/src/shell-integration/supported-shells/zsh.spec.js
index 4f1ca88..52e790f 100644
--- a/packages/safe-chain/src/shell-integration/supported-shells/zsh.spec.js
+++ b/packages/safe-chain/src/shell-integration/supported-shells/zsh.spec.js
@@ -206,6 +206,17 @@ describe("Zsh shell integration", () => {
       const content = fs.readFileSync(mockStartupFile, "utf-8");
       assert.ok(!content.includes("SAFE_CHAIN_DIR"));
     });
+
+    it("should show custom manual teardown instructions when custom dir is set", () => {
+      getSafeChainDirResult = "/custom/safe-chain";
+
+      assert.deepStrictEqual(zsh.getManualTeardownInstructions(), [
+        "Remove the following line from your ~/.zshrc file:",
+        '  export SAFE_CHAIN_DIR="/custom/safe-chain"',
+        "  source /test-home/.safe-chain/scripts/init-posix.sh",
+        "Then restart your terminal or run: source ~/.zshrc",
+      ]);
+    });
   });
 
   describe("integration tests", () => {