diff --git a/README.md b/README.md
index d5270e5..4daf1d2 100644
--- a/README.md
+++ b/README.md
@@ -202,7 +202,7 @@ You can set the minimum package age through multiple sources (in order of priori
    npm install express
    ```
 
-3. **Config File** (`~/.aikido/config.json`):
+3. **Config File** (`~/.safe-chain/config.json`):
 
    ```json
    {
@@ -246,7 +246,7 @@ You can set custom registries through environment variable or config file. Both
    export SAFE_CHAIN_PIP_CUSTOM_REGISTRIES="pip.company.com,registry.internal.net"
    ```
 
-2. **Config File** (`~/.aikido/config.json`):
+2. **Config File** (`~/.safe-chain/config.json`):
 
    ```json
    {
diff --git a/packages/safe-chain/src/config/configFile.js b/packages/safe-chain/src/config/configFile.js
index fd6ac26..bc4dc94 100644
--- a/packages/safe-chain/src/config/configFile.js
+++ b/packages/safe-chain/src/config/configFile.js
@@ -252,7 +252,30 @@ function getDatabaseVersionPath() {
  * @returns {string}
  */
 function getConfigFilePath() {
-  return path.join(getAikidoDirectory(), "config.json");
+  const primaryPath = path.join(getSafeChainDirectory(), "config.json");
+  if (fs.existsSync(primaryPath)) {
+    return primaryPath;
+  }
+
+  const legacyPath = path.join(getAikidoDirectory(), "config.json");
+  if (fs.existsSync(legacyPath)) {
+    return legacyPath;
+  }
+
+  return primaryPath;
+}
+
+/**
+ * @returns {string}
+ */
+function getSafeChainDirectory() {
+  const homeDir = os.homedir();
+  const safeChainDir = path.join(homeDir, ".safe-chain");
+
+  if (!fs.existsSync(safeChainDir)) {
+    fs.mkdirSync(safeChainDir, { recursive: true });
+  }
+  return safeChainDir;
 }
 
 /**
diff --git a/packages/safe-chain/src/config/configFile.spec.js b/packages/safe-chain/src/config/configFile.spec.js
index eff4048..8b36ff2 100644
--- a/packages/safe-chain/src/config/configFile.spec.js
+++ b/packages/safe-chain/src/config/configFile.spec.js
@@ -1,16 +1,35 @@
 import { describe, it, beforeEach, afterEach, mock } from "node:test";
 import assert from "node:assert";
+import os from "os";
+import path from "path";
 
-let configFileContent = undefined;
+const safeChainConfigPath = path.join(os.homedir(), ".safe-chain", "config.json");
+const aikidoConfigPath = path.join(os.homedir(), ".aikido", "config.json");
+
+/** @type {Map<string, string>} */
+let mockFiles = new Map();
 mock.module("fs", {
   namedExports: {
-    existsSync: () => configFileContent !== undefined,
-    readFileSync: () => configFileContent,
-    writeFileSync: (content) => (configFileContent = content),
+    existsSync: (filePath) => mockFiles.has(filePath),
+    readFileSync: (filePath) => {
+      if (!mockFiles.has(filePath)) {
+        throw new Error(`ENOENT: no such file: ${filePath}`);
+      }
+      return mockFiles.get(filePath);
+    },
+    writeFileSync: (filePath, content) => mockFiles.set(filePath, content),
     mkdirSync: () => {},
   },
 });
 
+/**
+ * Helper to set config content at the primary (~/.safe-chain/) location.
+ * @param {string} content
+ */
+function setConfigContent(content) {
+  mockFiles.set(safeChainConfigPath, content);
+}
+
 describe("getScanTimeout", async () => {
   let originalEnv;
 
@@ -29,12 +48,11 @@ describe("getScanTimeout", async () => {
       delete process.env.AIKIDO_SCAN_TIMEOUT_MS;
     }
 
-    configFileContent = undefined;
+    mockFiles.clear();
   });
 
   it("should return default timeout of 10000ms when no config or env var is set", () => {
     delete process.env.AIKIDO_SCAN_TIMEOUT_MS;
-    configFileContent = undefined;
 
     const timeout = getScanTimeout();
 
@@ -43,7 +61,7 @@ describe("getScanTimeout", async () => {
 
   it("should return timeout from config file when set", () => {
     delete process.env.AIKIDO_SCAN_TIMEOUT_MS;
-    configFileContent = JSON.stringify({ scanTimeout: 5000 });
+    setConfigContent(JSON.stringify({ scanTimeout: 5000 }));
 
     const timeout = getScanTimeout();
 
@@ -52,7 +70,7 @@ describe("getScanTimeout", async () => {
 
   it("should prioritize environment variable over config file", () => {
     process.env.AIKIDO_SCAN_TIMEOUT_MS = "20000";
-    configFileContent = JSON.stringify({ scanTimeout: 5000 });
+    setConfigContent(JSON.stringify({ scanTimeout: 5000 }));
 
     const timeout = getScanTimeout();
 
@@ -61,7 +79,7 @@ describe("getScanTimeout", async () => {
 
   it("should handle invalid environment variable and fall back to config", () => {
     process.env.AIKIDO_SCAN_TIMEOUT_MS = "invalid";
-    configFileContent = JSON.stringify({ scanTimeout: 7000 });
+    setConfigContent(JSON.stringify({ scanTimeout: 7000 }));
 
     const timeout = getScanTimeout();
 
@@ -69,8 +87,6 @@ describe("getScanTimeout", async () => {
   });
 
   it("should ignore zero and negative values and fall back to default", () => {
-    configFileContent = undefined;
-
     process.env.AIKIDO_SCAN_TIMEOUT_MS = "0";
 
     let timeout = getScanTimeout();
@@ -84,7 +100,7 @@ describe("getScanTimeout", async () => {
 
   it("should ignore textual non-numeric values in environment variable and fall back to config", () => {
     process.env.AIKIDO_SCAN_TIMEOUT_MS = "fast";
-    configFileContent = JSON.stringify({ scanTimeout: 8000 });
+    setConfigContent(JSON.stringify({ scanTimeout: 8000 }));
 
     const timeout = getScanTimeout();
 
@@ -93,7 +109,7 @@ describe("getScanTimeout", async () => {
 
   it("should ignore textual non-numeric values in config file and fall back to default", () => {
     delete process.env.AIKIDO_SCAN_TIMEOUT_MS;
-    configFileContent = JSON.stringify({ scanTimeout: "slow" });
+    setConfigContent(JSON.stringify({ scanTimeout: "slow" }));
 
     const timeout = getScanTimeout();
 
@@ -102,7 +118,7 @@ describe("getScanTimeout", async () => {
 
   it("should ignore textual non-numeric values in both env and config, fall back to default", () => {
     process.env.AIKIDO_SCAN_TIMEOUT_MS = "quick";
-    configFileContent = JSON.stringify({ scanTimeout: "medium" });
+    setConfigContent(JSON.stringify({ scanTimeout: "medium" }));
 
     const timeout = getScanTimeout();
 
@@ -111,7 +127,7 @@ describe("getScanTimeout", async () => {
 
   it("should ignore mixed alphanumeric strings in environment variable", () => {
     process.env.AIKIDO_SCAN_TIMEOUT_MS = "5000ms";
-    configFileContent = JSON.stringify({ scanTimeout: 6000 });
+    setConfigContent(JSON.stringify({ scanTimeout: 6000 }));
 
     const timeout = getScanTimeout();
 
@@ -120,7 +136,7 @@ describe("getScanTimeout", async () => {
 
   it("should ignore mixed alphanumeric strings in config file", () => {
     delete process.env.AIKIDO_SCAN_TIMEOUT_MS;
-    configFileContent = JSON.stringify({ scanTimeout: "3000ms" });
+    setConfigContent(JSON.stringify({ scanTimeout: "3000ms" }));
 
     const timeout = getScanTimeout();
 
@@ -132,19 +148,17 @@ describe("getMinimumPackageAgeHours", async () => {
   const { getMinimumPackageAgeHours } = await import("./configFile.js");
 
   afterEach(() => {
-    configFileContent = undefined;
+    mockFiles.clear();
   });
 
   it("should return null when config file doesn't exist", () => {
-    configFileContent = undefined;
-
     const hours = getMinimumPackageAgeHours();
 
     assert.strictEqual(hours, undefined);
   });
 
   it("should return null when config file exists but minimumPackageAgeHours is not set", () => {
-    configFileContent = JSON.stringify({ scanTimeout: 5000 });
+    setConfigContent(JSON.stringify({ scanTimeout: 5000 }));
 
     const hours = getMinimumPackageAgeHours();
 
@@ -152,7 +166,7 @@ describe("getMinimumPackageAgeHours", async () => {
   });
 
   it("should return value from config file when set to valid number", () => {
-    configFileContent = JSON.stringify({ minimumPackageAgeHours: 48 });
+    setConfigContent(JSON.stringify({ minimumPackageAgeHours: 48 }));
 
     const hours = getMinimumPackageAgeHours();
 
@@ -160,7 +174,7 @@ describe("getMinimumPackageAgeHours", async () => {
   });
 
   it("should handle string numbers in config file", () => {
-    configFileContent = JSON.stringify({ minimumPackageAgeHours: "72" });
+    setConfigContent(JSON.stringify({ minimumPackageAgeHours: "72" }));
 
     const hours = getMinimumPackageAgeHours();
 
@@ -168,7 +182,7 @@ describe("getMinimumPackageAgeHours", async () => {
   });
 
   it("should handle decimal values", () => {
-    configFileContent = JSON.stringify({ minimumPackageAgeHours: 1.5 });
+    setConfigContent(JSON.stringify({ minimumPackageAgeHours: 1.5 }));
 
     const hours = getMinimumPackageAgeHours();
 
@@ -176,7 +190,7 @@ describe("getMinimumPackageAgeHours", async () => {
   });
 
   it("should return null for non-numeric strings", () => {
-    configFileContent = JSON.stringify({ minimumPackageAgeHours: "invalid" });
+    setConfigContent(JSON.stringify({ minimumPackageAgeHours: "invalid" }));
 
     const hours = getMinimumPackageAgeHours();
 
@@ -184,7 +198,7 @@ describe("getMinimumPackageAgeHours", async () => {
   });
 
   it("should return undefined for values with units suffix", () => {
-    configFileContent = JSON.stringify({ minimumPackageAgeHours: "48h" });
+    setConfigContent(JSON.stringify({ minimumPackageAgeHours: "48h" }));
 
     const hours = getMinimumPackageAgeHours();
 
@@ -192,7 +206,7 @@ describe("getMinimumPackageAgeHours", async () => {
   });
 
   it("should handle malformed JSON and return null", () => {
-    configFileContent = "{ invalid json";
+    setConfigContent("{ invalid json");
 
     const hours = getMinimumPackageAgeHours();
 
@@ -200,7 +214,7 @@ describe("getMinimumPackageAgeHours", async () => {
   });
 
   it("should return 0 when minimumPackageAgeHours is set to 0", () => {
-    configFileContent = JSON.stringify({ minimumPackageAgeHours: 0 });
+    setConfigContent(JSON.stringify({ minimumPackageAgeHours: 0 }));
 
     const hours = getMinimumPackageAgeHours();
 
@@ -208,7 +222,7 @@ describe("getMinimumPackageAgeHours", async () => {
   });
 
   it("should return 0 when minimumPackageAgeHours is set to string '0'", () => {
-    configFileContent = JSON.stringify({ minimumPackageAgeHours: "0" });
+    setConfigContent(JSON.stringify({ minimumPackageAgeHours: "0" }));
 
     const hours = getMinimumPackageAgeHours();
 
@@ -216,7 +230,7 @@ describe("getMinimumPackageAgeHours", async () => {
   });
 
   it("should handle negative numeric values", () => {
-    configFileContent = JSON.stringify({ minimumPackageAgeHours: -24 });
+    setConfigContent(JSON.stringify({ minimumPackageAgeHours: -24 }));
 
     const hours = getMinimumPackageAgeHours();
 
@@ -224,7 +238,7 @@ describe("getMinimumPackageAgeHours", async () => {
   });
 
   it("should handle negative string values", () => {
-    configFileContent = JSON.stringify({ minimumPackageAgeHours: "-48" });
+    setConfigContent(JSON.stringify({ minimumPackageAgeHours: "-48" }));
 
     const hours = getMinimumPackageAgeHours();
 
@@ -249,19 +263,17 @@ for (const { packageManager, getCustomRegistries } of [
 {
   describe(getCustomRegistries.name, async () => {
     afterEach(() => {
-      configFileContent = undefined;
+      mockFiles.clear();
     });
 
     it("should return empty array when config file doesn't exist", () => {
-      configFileContent = undefined;
-
       const registries = getCustomRegistries();
 
       assert.deepStrictEqual(registries, []);
     });
 
     it(`should return empty array when ${packageManager} config is not set`, () => {
-      configFileContent = JSON.stringify({ scanTimeout: 5000 });
+      setConfigContent(JSON.stringify({ scanTimeout: 5000 }));
 
       const registries = getCustomRegistries();
 
@@ -269,9 +281,9 @@ for (const { packageManager, getCustomRegistries } of [
     });
 
     it("should return empty array when customRegistries is not an array", () => {
-      configFileContent = JSON.stringify({
+      setConfigContent(JSON.stringify({
         [packageManager]: { customRegistries: "not-an-array" },
-      });
+      }));
 
       const registries = getCustomRegistries();
 
@@ -279,11 +291,11 @@ for (const { packageManager, getCustomRegistries } of [
     });
 
     it("should return array of custom registries when set", () => {
-      configFileContent = JSON.stringify({
+      setConfigContent(JSON.stringify({
         [packageManager]: {
           customRegistries: [`${packageManager}.company.com`, "registry.internal.net"],
         },
-      });
+      }));
 
       const registries = getCustomRegistries();
 
@@ -294,7 +306,7 @@ for (const { packageManager, getCustomRegistries } of [
     });
 
     it("should filter out non-string values", () => {
-      configFileContent = JSON.stringify({
+      setConfigContent(JSON.stringify({
         [packageManager]: {
           customRegistries: [
             `${packageManager}.company.com`,
@@ -305,7 +317,7 @@ for (const { packageManager, getCustomRegistries } of [
             {},
           ],
         },
-      });
+      }));
 
       const registries = getCustomRegistries();
 
@@ -316,9 +328,9 @@ for (const { packageManager, getCustomRegistries } of [
     });
 
     it("should return empty array for empty customRegistries array", () => {
-      configFileContent = JSON.stringify({
+      setConfigContent(JSON.stringify({
         [packageManager]: { customRegistries: [] },
-      });
+      }));
 
       const registries = getCustomRegistries();
 
@@ -326,7 +338,7 @@ for (const { packageManager, getCustomRegistries } of [
     });
 
     it("should handle malformed JSON and return empty array", () => {
-      configFileContent = "{ invalid json";
+      setConfigContent("{ invalid json");
 
       const registries = getCustomRegistries();
 
@@ -334,3 +346,35 @@ for (const { packageManager, getCustomRegistries } of [
     });
   });
 }
+
+describe("config file location fallback", async () => {
+  const { getScanTimeout } = await import("./configFile.js");
+
+  afterEach(() => {
+    mockFiles.clear();
+    delete process.env.AIKIDO_SCAN_TIMEOUT_MS;
+  });
+
+  it("should read config from ~/.safe-chain/config.json when it exists", () => {
+    mockFiles.set(safeChainConfigPath, JSON.stringify({ scanTimeout: 3000 }));
+
+    assert.strictEqual(getScanTimeout(), 3000);
+  });
+
+  it("should fall back to ~/.aikido/config.json when primary does not exist", () => {
+    mockFiles.set(aikidoConfigPath, JSON.stringify({ scanTimeout: 4000 }));
+
+    assert.strictEqual(getScanTimeout(), 4000);
+  });
+
+  it("should prefer ~/.safe-chain/config.json when both exist", () => {
+    mockFiles.set(safeChainConfigPath, JSON.stringify({ scanTimeout: 3000 }));
+    mockFiles.set(aikidoConfigPath, JSON.stringify({ scanTimeout: 4000 }));
+
+    assert.strictEqual(getScanTimeout(), 3000);
+  });
+
+  it("should return default when neither config file exists", () => {
+    assert.strictEqual(getScanTimeout(), 10000);
+  });
+});
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 a2a3739..07d89cb 100644
--- a/packages/safe-chain/src/shell-integration/supported-shells/bash.js
+++ b/packages/safe-chain/src/shell-integration/supported-shells/bash.js
@@ -32,7 +32,7 @@ function teardown(tools) {
     );
   }
 
-  // Removes the line that sources the safe-chain bash initialization script (~/.aikido/scripts/init-posix.sh)
+  // Removes the line that sources the safe-chain bash initialization script (~/.safe-chain/scripts/init-posix.sh)
   removeLinesMatchingPattern(
     startupFile,
     /^source\s+~\/\.safe-chain\/scripts\/init-posix\.sh/,
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 fc2b807..6086095 100644
--- a/packages/safe-chain/src/shell-integration/supported-shells/zsh.js
+++ b/packages/safe-chain/src/shell-integration/supported-shells/zsh.js
@@ -31,7 +31,7 @@ function teardown(tools) {
     );
   }
 
-  // Removes the line that sources the safe-chain zsh initialization script (~/.aikido/scripts/init-posix.sh)
+  // Removes the line that sources the safe-chain zsh initialization script (~/.safe-chain/scripts/init-posix.sh)
   removeLinesMatchingPattern(
     startupFile,
     /^source\s+~\/\.safe-chain\/scripts\/init-posix\.sh/,