diff --git a/tests/hooks/bash-hook-dispatcher.test.js b/tests/hooks/bash-hook-dispatcher.test.js
index 893b45d5b..2f98d7aeb 100644
--- a/tests/hooks/bash-hook-dispatcher.test.js
+++ b/tests/hooks/bash-hook-dispatcher.test.js
@@ -11,6 +11,13 @@ const { spawnSync } = require('child_process');
 const preDispatcher = path.join(__dirname, '..', '..', 'scripts', 'hooks', 'pre-bash-dispatcher.js');
 const postDispatcher = path.join(__dirname, '..', '..', 'scripts', 'hooks', 'post-bash-dispatcher.js');
 
+// The post-Bash dispatcher appends to ~/.claude/bash-commands.log and
+// ~/.claude/cost-tracker.log, so runs get an empty home instead of the
+// developer's real one unless a test passes its own HOME.
+const ISOLATED_HOME = fs.mkdtempSync(path.join(os.tmpdir(), 'ecc-bash-dispatcher-home-'));
+const ISOLATED_HOME_ENV = { HOME: ISOLATED_HOME, USERPROFILE: ISOLATED_HOME };
+process.on('exit', () => fs.rmSync(ISOLATED_HOME, { recursive: true, force: true }));
+
 function test(name, fn) {
   try {
     fn();
@@ -29,6 +36,7 @@ function runScript(scriptPath, input, env = {}) {
     encoding: 'utf8',
     env: {
       ...process.env,
+      ...ISOLATED_HOME_ENV,
       ...env,
     },
     timeout: 10000,
diff --git a/tests/hooks/cost-tracker.test.js b/tests/hooks/cost-tracker.test.js
index ef6e2463f..40805ee77 100644
--- a/tests/hooks/cost-tracker.test.js
+++ b/tests/hooks/cost-tracker.test.js
@@ -15,6 +15,12 @@ const script = path.join(__dirname, '..', '..', 'scripts', 'hooks', 'cost-tracke
 
 // Harness caches belong to a real private root shared by parent and hook child.
 const cacheRoot = fs.realpathSync(fs.mkdtempSync(path.join(os.tmpdir(), 'ecc-cost-cache-')));
+// cost-tracker.js appends to ~/.claude/metrics/costs.jsonl and writes cost
+// snapshots there, so runs get an empty home instead of the developer's real
+// one unless a test passes withTempHome().
+const ISOLATED_HOME = fs.mkdtempSync(path.join(os.tmpdir(), 'ecc-cost-home-'));
+const ISOLATED_HOME_ENV = { HOME: ISOLATED_HOME, USERPROFILE: ISOLATED_HOME };
+process.on('exit', () => fs.rmSync(ISOLATED_HOME, { recursive: true, force: true }));
 const savedTempEnvironment = Object.fromEntries(['TMPDIR', 'TMP', 'TEMP']
   .map(name => [name, process.env[name]]));
 for (const name of Object.keys(savedTempEnvironment)) process.env[name] = cacheRoot;
@@ -56,7 +62,7 @@ function runScript(input, envOverrides = {}) {
     encoding: 'utf8',
     input: inputStr,
     timeout: 10000,
-    env: { ...process.env, ...envOverrides, TMPDIR: cacheRoot, TMP: cacheRoot, TEMP: cacheRoot },
+    env: { ...process.env, ...ISOLATED_HOME_ENV, ...envOverrides, TMPDIR: cacheRoot, TMP: cacheRoot, TEMP: cacheRoot },
   });
   return { code: result.status || 0, stdout: result.stdout || '', stderr: result.stderr || '' };
 }
diff --git a/tests/hooks/evaluate-session.test.js b/tests/hooks/evaluate-session.test.js
index f49bb6a4b..45a69c0b8 100644
--- a/tests/hooks/evaluate-session.test.js
+++ b/tests/hooks/evaluate-session.test.js
@@ -15,6 +15,16 @@ const { spawnSync } = require('child_process');
 
 const evaluateScript = path.join(__dirname, '..', '..', 'scripts', 'hooks', 'evaluate-session.js');
 
+// evaluate-session.js creates its learned-skills directory under the home
+// directory, so every run gets an empty home instead of the developer's real one.
+const ISOLATED_HOME = fs.mkdtempSync(path.join(os.tmpdir(), 'eval-session-home-'));
+const ISOLATED_HOME_ENV = { HOME: ISOLATED_HOME, USERPROFILE: ISOLATED_HOME };
+process.on('exit', () => fs.rmSync(ISOLATED_HOME, { recursive: true, force: true }));
+
+function isolatedEnv(extra = {}) {
+  return { ...process.env, ...ISOLATED_HOME_ENV, ...extra };
+}
+
 // Test helpers
 function test(name, fn) {
   try {
@@ -62,6 +72,7 @@ function runEvaluate(stdinJson) {
     encoding: 'utf8',
     input: JSON.stringify(stdinJson),
     timeout: 10000,
+    env: isolatedEnv(),
   });
   return {
     code: result.status || 0,
@@ -135,6 +146,7 @@ function runTests() {
       encoding: 'utf8',
       input: 'not valid json at all',
       timeout: 10000,
+      env: isolatedEnv(),
     });
     assert.strictEqual(result.status, 0, 'Should exit 0 even on bad stdin');
   })) passed++; else failed++;
@@ -253,6 +265,7 @@ function runTests() {
       encoding: 'utf8',
       input: '',
       timeout: 10000,
+      env: isolatedEnv(),
     });
     // Empty stdin → JSON.parse('') throws → fallback to env var (unset) → null → exit 0
     assert.strictEqual(result.status, 0, 'Should exit 0 on empty stdin');
@@ -269,7 +282,7 @@ function runTests() {
       encoding: 'utf8',
       input: 'invalid json {{{',
       timeout: 10000,
-      env: { ...process.env, CLAUDE_TRANSCRIPT_PATH: transcript }
+      env: isolatedEnv({ CLAUDE_TRANSCRIPT_PATH: transcript })
     });
 
     assert.strictEqual(result.status, 0, 'Should exit 0');
@@ -396,8 +409,8 @@ function runTests() {
         'Should NOT contain literal ~ in output (should be expanded)');
       assert.ok(result.stderr.includes('custom-learned-skills-dir'),
         `Should reference the custom learned skills dir. Got: ${result.stderr}`);
-      // The ~ should have been replaced with os.homedir()
-      assert.ok(result.stderr.includes(os.homedir()),
+      // The ~ should have been replaced with the child's home directory
+      assert.ok(result.stderr.includes(ISOLATED_HOME),
         `Should contain expanded home directory. Got: ${result.stderr}`);
 
       cleanupTestDir(testDir);
diff --git a/tests/hooks/hooks.test.js b/tests/hooks/hooks.test.js
index e31cdf449..db469d34d 100644
--- a/tests/hooks/hooks.test.js
+++ b/tests/hooks/hooks.test.js
@@ -177,12 +177,19 @@ async function asyncTest(name, fn) {
   }
 }
 
+// Hook scripts write session files, compaction logs, learned skills and
+// homunculus data under the home directory, so script runs get an empty home
+// instead of the developer's real one unless a test passes its own HOME.
+const ISOLATED_HOME = fs.mkdtempSync(path.join(os.tmpdir(), 'hooks-test-home-'));
+const ISOLATED_HOME_ENV = { HOME: ISOLATED_HOME, USERPROFILE: ISOLATED_HOME };
+process.on('exit', () => fs.rmSync(ISOLATED_HOME, { recursive: true, force: true }));
+
 // Run a script and capture output
 function runScript(scriptPath, input = '', env = {}, cwd = process.cwd()) {
   return new Promise((resolve, reject) => {
     const proc = spawn('node', [scriptPath], {
       cwd,
-      env: { ...process.env, ...env },
+      env: { ...process.env, ...ISOLATED_HOME_ENV, ...env },
       stdio: ['pipe', 'pipe', 'pipe']
     });
 
@@ -209,7 +216,7 @@ function runShellScript(scriptPath, args = [], input = '', env = {}, cwd = proce
   return new Promise((resolve, reject) => {
     const proc = spawn('bash', [toBashPath(scriptPath), ...args], {
       cwd,
-      env: { ...process.env, ...env },
+      env: { ...process.env, ...ISOLATED_HOME_ENV, ...env },
       stdio: ['pipe', 'pipe', 'pipe']
     });
 
@@ -1515,7 +1522,7 @@ async function runTests() {
   if (
     await asyncTest('creates compaction log', async () => {
       await runScript(path.join(scriptsDir, 'pre-compact.js'));
-      const logFile = path.join(getCanonicalSessionsDir(os.homedir()), 'compaction-log.txt');
+      const logFile = path.join(getCanonicalSessionsDir(ISOLATED_HOME), 'compaction-log.txt');
       assert.ok(fs.existsSync(logFile), 'Compaction log should exist');
     })
   )
@@ -3700,7 +3707,7 @@ async function runTests() {
 
       const shell = process.platform === 'win32' ? 'bash' : 'bash';
       const proc = spawn(shell, ['-lc', shellCommand], {
-        env: process.env,
+        env: { ...process.env, ...ISOLATED_HOME_ENV },
         stdio: ['ignore', 'pipe', 'pipe']
       });
 
diff --git a/tests/hooks/session-activity-tracker.test.js b/tests/hooks/session-activity-tracker.test.js
index bd541c454..d00ea4295 100644
--- a/tests/hooks/session-activity-tracker.test.js
+++ b/tests/hooks/session-activity-tracker.test.js
@@ -47,13 +47,20 @@ function withTempHome(homeDir) {
   };
 }
 
+// session-activity-tracker.js appends to ~/.claude/metrics/tool-usage.jsonl, so
+// runs get an empty home instead of the developer's real one unless a test
+// passes withTempHome().
+const ISOLATED_HOME = fs.mkdtempSync(path.join(os.tmpdir(), 'session-activity-home-'));
+const ISOLATED_HOME_ENV = { HOME: ISOLATED_HOME, USERPROFILE: ISOLATED_HOME };
+process.on('exit', () => fs.rmSync(ISOLATED_HOME, { recursive: true, force: true }));
+
 function runScript(input, envOverrides = {}, options = {}) {
   const inputStr = typeof input === 'string' ? input : JSON.stringify(input);
   const result = spawnSync('node', [script], {
     encoding: 'utf8',
     input: inputStr,
     timeout: 10000,
-    env: { ...process.env, ...envOverrides },
+    env: { ...process.env, ...ISOLATED_HOME_ENV, ...envOverrides },
     cwd: options.cwd,
   });
   return { code: result.status || 0, stdout: result.stdout || '', stderr: result.stderr || '' };
diff --git a/tests/hooks/stop-hooks-stdout.test.js b/tests/hooks/stop-hooks-stdout.test.js
index e834eb222..785f6a884 100644
--- a/tests/hooks/stop-hooks-stdout.test.js
+++ b/tests/hooks/stop-hooks-stdout.test.js
@@ -31,6 +31,9 @@ const SUBPROCESS_TIMEOUT_MS = process.platform === 'darwin' && process.env.CI ==
 
 const workDir = fs.mkdtempSync(path.join(os.tmpdir(), 'ecc-stop-stdout-')); // non-git cwd
 const dataHome = fs.mkdtempSync(path.join(os.tmpdir(), 'ecc-stop-data-'));
+// Stop hooks also write learned skills under the home directory; give them
+// an empty one instead of the developer's real one.
+const homeDir = fs.mkdtempSync(path.join(os.tmpdir(), 'ecc-stop-home-'));
 
 function test(name, fn) {
   try {
@@ -58,6 +61,8 @@ function stopPayload(messageCharacters, character = 'm') {
 function hookEnv() {
   const env = {
     ...process.env,
+    HOME: homeDir,
+    USERPROFILE: homeDir,
     ECC_HOOK_PROFILE: 'standard',
     ECC_AGENT_DATA_HOME: dataHome,
     CLAUDE_SESSION_ID: `stop-stdout-test-${process.pid}`
@@ -448,6 +453,7 @@ else failed++;
 try {
   fs.rmSync(workDir, { recursive: true, force: true });
   fs.rmSync(dataHome, { recursive: true, force: true });
+  fs.rmSync(homeDir, { recursive: true, force: true });
 } catch {
   /* best-effort cleanup */
 }
diff --git a/tests/integration/hooks.test.js b/tests/integration/hooks.test.js
index 96ad9b4d1..55722eca3 100644
--- a/tests/integration/hooks.test.js
+++ b/tests/integration/hooks.test.js
@@ -41,6 +41,13 @@ async function asyncTest(name, fn) {
   }
 }
 
+// Hook scripts write session data, learned skills and homunculus observations
+// under the home directory, so runs get an empty home instead of the developer's
+// real one unless a test passes its own HOME.
+const ISOLATED_HOME = fs.mkdtempSync(path.join(os.tmpdir(), 'ecc-integration-home-'));
+const ISOLATED_HOME_ENV = { HOME: ISOLATED_HOME, USERPROFILE: ISOLATED_HOME };
+process.on('exit', () => fs.rmSync(ISOLATED_HOME, { recursive: true, force: true }));
+
 /**
  * Run a hook script with simulated Claude Code input
  * @param {string} scriptPath - Path to the hook script
@@ -51,7 +58,7 @@ async function asyncTest(name, fn) {
 function runHookWithInput(scriptPath, input = {}, env = {}, timeoutMs = 10000) {
   return new Promise((resolve, reject) => {
     const proc = spawn('node', [scriptPath], {
-      env: { ...process.env, ...env },
+      env: { ...process.env, ...ISOLATED_HOME_ENV, ...env },
       stdio: ['pipe', 'pipe', 'pipe']
     });
 
@@ -110,7 +117,7 @@ function getSessionStartPayload(stdout) {
 function runHookCommand(command, input = {}, env = {}, timeoutMs = 10000) {
   return new Promise((resolve, reject) => {
     const isWindows = process.platform === 'win32';
-    const mergedEnv = { ...process.env, CLAUDE_PLUGIN_ROOT: REPO_ROOT, ...env };
+    const mergedEnv = { ...process.env, ...ISOLATED_HOME_ENV, CLAUDE_PLUGIN_ROOT: REPO_ROOT, ...env };
     if (Array.isArray(command)) {
       const [program, ...args] = command;
       const proc = spawn(program, args, { env: mergedEnv, stdio: ['pipe', 'pipe', 'pipe'] });
@@ -297,6 +304,7 @@ async function runTests() {
 
   if (await asyncTest('hooks handle malformed JSON input', async () => {
     const proc = spawn('node', [path.join(scriptsDir, 'session-start.js')], {
+      env: { ...process.env, ...ISOLATED_HOME_ENV },
       stdio: ['pipe', 'pipe', 'pipe']
     });
 
@@ -887,6 +895,7 @@ async function runTests() {
     // session-end parses stdin JSON. If input is > 1MB and truncated mid-JSON,
     // JSON.parse should fail and fall back to env var
     const proc = spawn('node', [path.join(scriptsDir, 'session-end.js')], {
+      env: { ...process.env, ...ISOLATED_HOME_ENV },
       stdio: ['pipe', 'pipe', 'pipe']
     });
 
diff --git a/tests/lib/package-manager.test.js b/tests/lib/package-manager.test.js
index 0a00caabd..8d6932eba 100644
--- a/tests/lib/package-manager.test.js
+++ b/tests/lib/package-manager.test.js
@@ -767,8 +767,8 @@ function runTests() {
   // setPreferredPackageManager success
   console.log('\nsetPreferredPackageManager (success):');
 
-  if (test('successfully saves preferred package manager', () => {
-    // This writes to ~/.claude/package-manager.json — read original to restore
+  if (test('successfully saves preferred package manager', () => withIsolatedHome(() => {
+    // Writes ~/.claude/package-manager.json under the isolated home, not the real one
     const utils = require('../../scripts/lib/utils');
     const configPath = path.join(utils.getClaudeDir(), 'package-manager.json');
     const original = utils.readFile(configPath);
@@ -791,7 +791,7 @@ function runTests() {
         }
       }
     }
-  })) passed++;
+  }))) passed++;
   else failed++;
 
   // getCommandPattern completeness
diff --git a/tests/pi/pi-extension-adapter.test.js b/tests/pi/pi-extension-adapter.test.js
index d03032baa..b900fc7d6 100644
--- a/tests/pi/pi-extension-adapter.test.js
+++ b/tests/pi/pi-extension-adapter.test.js
@@ -73,6 +73,13 @@ function stripComments(source) {
   return source.replace(/\/\*[\s\S]*?\*\//g, "").replace(/\/\/.*$/gm, "")
 }
 
+// Hook scripts write homunculus observations under the home directory, so
+// runner calls get an empty home instead of the developer's real one unless a
+// test passes its own HOME.
+const ISOLATED_HOME = fs.mkdtempSync(path.join(os.tmpdir(), "ecc-pi-home-"))
+const ISOLATED_HOME_ENV = { HOME: ISOLATED_HOME, USERPROFILE: ISOLATED_HOME }
+process.on("exit", () => fs.rmSync(ISOLATED_HOME, { recursive: true, force: true }))
+
 /**
  * Invokes ECC's hook runner like the adapter (`runEccHook` in
  * .pi/extensions/index.ts): it uses the test host's Node executable with the
@@ -85,7 +92,7 @@ function runHookRunner(eccRoot, hookId, relScript, profiles, payload, extraEnv,
     encoding: "utf8",
     cwd: cwd || eccRoot,
     timeout: 30000,
-    env: { ...process.env, CLAUDE_PLUGIN_ROOT: eccRoot, ECC_PLUGIN_ROOT: eccRoot, ...extraEnv },
+    env: { ...process.env, ...ISOLATED_HOME_ENV, CLAUDE_PLUGIN_ROOT: eccRoot, ECC_PLUGIN_ROOT: eccRoot, ...extraEnv },
   })
 }