diff --git a/apps/cli/src/commands/eval/last-config.ts b/apps/cli/src/commands/eval/last-config.ts
index 37dd7cf44..44402a4e3 100644
--- a/apps/cli/src/commands/eval/last-config.ts
+++ b/apps/cli/src/commands/eval/last-config.ts
@@ -1,9 +1,9 @@
 import { mkdir, readFile, writeFile } from 'node:fs/promises';
 import path from 'node:path';
-import { getAgentvHome } from '@agentv/core';
+import { getAgentvConfigDir } from '@agentv/core';
 
-const AGENTV_DIR = getAgentvHome();
-const LAST_CONFIG_PATH = path.join(AGENTV_DIR, 'last-config.json');
+const CONFIG_DIR = getAgentvConfigDir();
+const LAST_CONFIG_PATH = path.join(CONFIG_DIR, 'last-config.json');
 
 export interface LastConfig {
   readonly timestamp: string;
@@ -25,6 +25,6 @@ export async function loadLastConfig(): Promise<LastConfig | undefined> {
 }
 
 export async function saveLastConfig(config: LastConfig): Promise<void> {
-  await mkdir(AGENTV_DIR, { recursive: true });
+  await mkdir(CONFIG_DIR, { recursive: true });
   await writeFile(LAST_CONFIG_PATH, JSON.stringify(config, null, 2), 'utf-8');
 }
diff --git a/apps/cli/src/update-check.ts b/apps/cli/src/update-check.ts
index cae54fdb6..d50ad7751 100644
--- a/apps/cli/src/update-check.ts
+++ b/apps/cli/src/update-check.ts
@@ -1,10 +1,10 @@
 import { spawn } from 'node:child_process';
 import { readFile } from 'node:fs/promises';
 import { join } from 'node:path';
-import { getAgentvHome } from '@agentv/core';
+import { getAgentvConfigDir } from '@agentv/core';
 
 const CHECK_INTERVAL_MS = 24 * 60 * 60 * 1000; // 24 hours
-const AGENTV_DIR = getAgentvHome();
+const CONFIG_DIR = getAgentvConfigDir();
 const CACHE_FILE = 'version-check.json';
 const NPM_REGISTRY_URL = 'https://registry.npmjs.org/agentv/latest';
 
@@ -17,7 +17,7 @@ export interface UpdateCache {
  * Read the cached update info from disk. Returns null if missing or malformed.
  */
 export async function getCachedUpdateInfo(path?: string): Promise<UpdateCache | null> {
-  const filePath = path ?? join(AGENTV_DIR, CACHE_FILE);
+  const filePath = path ?? join(CONFIG_DIR, CACHE_FILE);
   try {
     const raw = await readFile(filePath, 'utf-8');
     const data = JSON.parse(raw);
@@ -67,7 +67,7 @@ export function buildNotice(currentVersion: string, latestVersion: string | null
  * survives even if the parent calls process.exit().
  */
 export function backgroundUpdateCheck(): void {
-  const dir = AGENTV_DIR;
+  const dir = CONFIG_DIR;
   const filePath = join(dir, CACHE_FILE);
 
   const script = `
diff --git a/apps/web/src/content/docs/docs/evaluation/running-evals.mdx b/apps/web/src/content/docs/docs/evaluation/running-evals.mdx
index efa3ddc8f..b0e46c911 100644
--- a/apps/web/src/content/docs/docs/evaluation/running-evals.mdx
+++ b/apps/web/src/content/docs/docs/evaluation/running-evals.mdx
@@ -409,7 +409,7 @@ The `{timestamp}` placeholder is replaced with an ISO-like timestamp (e.g., `202
 
 ### AGENTV_HOME
 
-Override the default `~/.agentv` directory for all global runtime data (workspaces, git cache, subagents, trace state, version check cache):
+Override the data directory for heavy runtime artifacts — workspaces, workspace pool, subagents, trace state, git cache, and downloaded dependencies. Lightweight config and cache files (`version-check.json`, `last-config.json`, `projects.yaml`) always stay in `~/.agentv` regardless of this setting.
 
 ```bash
 # Linux/macOS
diff --git a/packages/core/src/benchmarks.ts b/packages/core/src/benchmarks.ts
index 2fb603b12..53a8a2ed2 100644
--- a/packages/core/src/benchmarks.ts
+++ b/packages/core/src/benchmarks.ts
@@ -16,12 +16,20 @@
  * discoverBenchmarks() to scan a directory tree for `.agentv/` directories.
  */
 
-import { existsSync, mkdirSync, readFileSync, readdirSync, statSync, writeFileSync } from 'node:fs';
+import {
+  copyFileSync,
+  existsSync,
+  mkdirSync,
+  readFileSync,
+  readdirSync,
+  statSync,
+  writeFileSync,
+} from 'node:fs';
 import path from 'node:path';
 
 import { parse as parseYaml, stringify as stringifyYaml } from 'yaml';
 
-import { getAgentvHome } from './paths.js';
+import { getAgentvConfigDir, getAgentvHome } from './paths.js';
 
 // ── Types ───────────────────────────────────────────────────────────────
 
@@ -40,13 +48,31 @@ export interface BenchmarkRegistry {
 // ── Registry path ───────────────────────────────────────────────────────
 
 export function getBenchmarksRegistryPath(): string {
-  return path.join(getAgentvHome(), 'projects.yaml');
+  return path.join(getAgentvConfigDir(), 'projects.yaml');
+}
+
+/**
+ * One-time migration: if projects.yaml exists at the old AGENTV_HOME location
+ * but not in ~/.agentv, copy it over. This handles the case where users had
+ * AGENTV_HOME set and projects.yaml was created there before the config/data split.
+ */
+function migrateProjectsYaml(targetPath: string): void {
+  const dataHome = getAgentvHome();
+  const configDir = getAgentvConfigDir();
+  if (dataHome === configDir) return;
+  const legacyPath = path.join(dataHome, 'projects.yaml');
+  if (!existsSync(legacyPath)) return;
+  mkdirSync(path.dirname(targetPath), { recursive: true });
+  copyFileSync(legacyPath, targetPath);
 }
 
 // ── Load / Save ─────────────────────────────────────────────────────────
 
 export function loadBenchmarkRegistry(): BenchmarkRegistry {
   const registryPath = getBenchmarksRegistryPath();
+  if (!existsSync(registryPath)) {
+    migrateProjectsYaml(registryPath);
+  }
   if (!existsSync(registryPath)) {
     return { benchmarks: [] };
   }
diff --git a/packages/core/src/index.ts b/packages/core/src/index.ts
index 79bf7066e..656fd4c26 100644
--- a/packages/core/src/index.ts
+++ b/packages/core/src/index.ts
@@ -73,6 +73,7 @@ export {
   type ResultsRepoStatus,
 } from './evaluation/results-repo.js';
 export {
+  getAgentvConfigDir,
   getAgentvHome,
   getWorkspacesRoot,
   getSubagentsRoot,
diff --git a/packages/core/src/paths.ts b/packages/core/src/paths.ts
index d23f41d65..e864319ca 100644
--- a/packages/core/src/paths.ts
+++ b/packages/core/src/paths.ts
@@ -3,6 +3,20 @@ import path from 'node:path';
 
 let logged = false;
 
+/**
+ * The default config directory (~/.agentv). Always resolves to the user's home
+ * directory regardless of AGENTV_HOME. Used for lightweight, machine-local files
+ * like version-check.json, last-config.json, and projects.yaml.
+ */
+export function getAgentvConfigDir(): string {
+  return path.join(os.homedir(), '.agentv');
+}
+
+/**
+ * The data root for heavy/large artifacts (workspaces, workspace-pool, subagents,
+ * trace-state, cache, deps). Respects AGENTV_HOME override so users can relocate
+ * bulky data to a different drive. Falls back to ~/.agentv when unset.
+ */
 export function getAgentvHome(): string {
   const envHome = process.env.AGENTV_HOME;
   if (envHome && envHome !== 'undefined') {
diff --git a/packages/core/test/paths.test.ts b/packages/core/test/paths.test.ts
index 484aac0ba..8de99b3c8 100644
--- a/packages/core/test/paths.test.ts
+++ b/packages/core/test/paths.test.ts
@@ -4,6 +4,7 @@ import path from 'node:path';
 
 import {
   _resetLoggedForTesting,
+  getAgentvConfigDir,
   getAgentvHome,
   getSubagentsRoot,
   getTraceStateRoot,
@@ -75,4 +76,13 @@ describe('paths', () => {
     expect(spy).not.toHaveBeenCalled();
     spy.mockRestore();
   });
+
+  it('getAgentvConfigDir always returns ~/.agentv regardless of AGENTV_HOME', () => {
+    process.env.AGENTV_HOME = '/data/agentv';
+    expect(getAgentvConfigDir()).toBe(path.join(os.homedir(), '.agentv'));
+  });
+
+  it('getAgentvConfigDir returns ~/.agentv when AGENTV_HOME is not set', () => {
+    expect(getAgentvConfigDir()).toBe(path.join(os.homedir(), '.agentv'));
+  });
 });