diff --git a/packages/cli/src/cli.tsx b/packages/cli/src/cli.tsx
index 552e4a23..b9170455 100644
--- a/packages/cli/src/cli.tsx
+++ b/packages/cli/src/cli.tsx
@@ -1,8 +1,7 @@
 import { render } from "ink";
 import { readFileSync } from "node:fs";
 import { join } from "node:path";
-import { homedir } from "node:os";
-import { setShellIfWindows, getProjectCode } from "@vegamo/deepcode-core";
+import { getProjectCode, getUserDataDir, setShellIfWindows } from "@vegamo/deepcode-core";
 import { checkForNpmUpdate, promptForPendingUpdate } from "./common/update-check";
 import { AppContainer } from "./ui";
 import { parseArguments } from "./cli-args";
@@ -36,7 +35,7 @@ async function main(): Promise<void> {
   // Resolve --last to the most recent session ID for the current project
   if (parsed.last) {
     const projectCode = getProjectCode(projectRoot);
-    const indexPath = join(homedir(), ".deepcode", "projects", projectCode, "sessions-index.json");
+    const indexPath = join(getUserDataDir(), "projects", projectCode, "sessions-index.json");
     try {
       const index = JSON.parse(readFileSync(indexPath, "utf-8"));
       const entries: { id: string; updateTime: string }[] = Array.isArray(index?.entries) ? index.entries : [];
@@ -54,7 +53,7 @@ async function main(): Promise<void> {
 
   if (forkSessionId === true) {
     const projectCode = getProjectCode(projectRoot);
-    const indexPath = join(homedir(), ".deepcode", "projects", projectCode, "sessions-index.json");
+    const indexPath = join(getUserDataDir(), "projects", projectCode, "sessions-index.json");
     try {
       const index = JSON.parse(readFileSync(indexPath, "utf-8"));
       const entries: { id: string; updateTime: string }[] = Array.isArray(index?.entries) ? index.entries : [];
@@ -88,7 +87,7 @@ async function main(): Promise<void> {
   // Validate --resume <sessionId> before entering TUI
   if (typeof resumeSessionId === "string") {
     const projectCode = getProjectCode(projectRoot);
-    const indexPath = join(homedir(), ".deepcode", "projects", projectCode, "sessions-index.json");
+    const indexPath = join(getUserDataDir(), "projects", projectCode, "sessions-index.json");
     try {
       const index = JSON.parse(readFileSync(indexPath, "utf-8"));
       const found =
@@ -105,7 +104,7 @@ async function main(): Promise<void> {
 
   if (typeof forkSessionId === "string") {
     const projectCode = getProjectCode(projectRoot);
-    const indexPath = join(homedir(), ".deepcode", "projects", projectCode, "sessions-index.json");
+    const indexPath = join(getUserDataDir(), "projects", projectCode, "sessions-index.json");
     try {
       const index = JSON.parse(readFileSync(indexPath, "utf-8"));
       const found = Array.isArray(index?.entries) && index.entries.some((e: { id: string }) => e.id === forkSessionId);
diff --git a/packages/cli/src/common/update-check.ts b/packages/cli/src/common/update-check.ts
index 2dad85f8..76e2a4ac 100644
--- a/packages/cli/src/common/update-check.ts
+++ b/packages/cli/src/common/update-check.ts
@@ -1,11 +1,10 @@
 import { spawn, type ChildProcess, type SpawnOptions } from "child_process";
 import React from "react";
 import * as fs from "fs";
-import * as os from "os";
 import * as path from "path";
 import { render, type Instance } from "ink";
 import { UpdatePrompt, type UpdatePromptChoice } from "../ui";
-import { killProcessTree } from "@vegamo/deepcode-core";
+import { getUserDataDir, killProcessTree } from "@vegamo/deepcode-core";
 import type { PackageJson } from "../utils/package";
 
 type UpdateState = {
@@ -118,7 +117,7 @@ export function compareVersions(a: string, b: string): number {
 }
 
 export function getUpdateStatePath(): string {
-  return path.join(os.homedir(), ".deepcode", UPDATE_STATE_FILE);
+  return path.join(getUserDataDir(), UPDATE_STATE_FILE);
 }
 
 async function promptUpdateChoice({
diff --git a/packages/core/src/common/debug-logger.ts b/packages/core/src/common/debug-logger.ts
index 124049e1..4ad615ef 100644
--- a/packages/core/src/common/debug-logger.ts
+++ b/packages/core/src/common/debug-logger.ts
@@ -1,6 +1,6 @@
 import * as fs from "fs";
-import * as os from "os";
 import * as path from "path";
+import { getUserDataDir } from "../settings";
 
 const DEBUG_LOG_FILE = "debug.log";
 
@@ -34,7 +34,7 @@ export function logOpenAIChatCompletionDebug(entry: OpenAIChatCompletionDebugEnt
 }
 
 export function getDebugLogPath(): string {
-  return path.join(os.homedir(), ".deepcode", "logs", DEBUG_LOG_FILE);
+  return path.join(getUserDataDir(), "logs", DEBUG_LOG_FILE);
 }
 
 export function normalizeDebugError(error: unknown): { name: string; message: string; stack?: string } {
diff --git a/packages/core/src/common/error-logger.ts b/packages/core/src/common/error-logger.ts
index 694a331a..de793afe 100644
--- a/packages/core/src/common/error-logger.ts
+++ b/packages/core/src/common/error-logger.ts
@@ -1,9 +1,9 @@
 import * as fs from "fs";
 import * as path from "path";
-import * as os from "os";
 import type { LlmErrorDetails } from "./llm-error";
+import { getUserDataDir } from "../settings";
 
-const LOG_DIR = path.join(os.homedir(), ".deepcode", "logs");
+const LOG_DIR = path.join(getUserDataDir(), "logs");
 const ERROR_LOG_PATH = path.join(LOG_DIR, "error.log");
 
 function ensureLogDir(): void {
diff --git a/packages/core/src/common/openai-client.ts b/packages/core/src/common/openai-client.ts
index d3b56c08..495f2f5f 100644
--- a/packages/core/src/common/openai-client.ts
+++ b/packages/core/src/common/openai-client.ts
@@ -3,7 +3,7 @@ import * as os from "os";
 import * as path from "path";
 import OpenAI from "openai";
 import { Agent, fetch as undiciFetch } from "undici";
-import { resolveCurrentSettings } from "../settings";
+import { getUserDataDir, resolveCurrentSettings } from "../settings";
 
 // Custom undici Agent with a 180-second keepAlive timeout.  The default
 // global fetch (undici) only keeps connections alive for 4 seconds, which
@@ -108,7 +108,7 @@ export function createOpenAIClient(projectRoot: string = process.cwd()): {
 
 function getMachineId(): string | undefined {
   try {
-    const idPath = path.join(os.homedir(), ".deepcode", "machine-id");
+    const idPath = path.join(getUserDataDir(), "machine-id");
     if (fs.existsSync(idPath)) {
       const raw = fs.readFileSync(idPath, "utf8").trim();
       if (raw) {
diff --git a/packages/core/src/index.ts b/packages/core/src/index.ts
index d389348c..1b6249c2 100644
--- a/packages/core/src/index.ts
+++ b/packages/core/src/index.ts
@@ -13,6 +13,8 @@ export {
   applyModelConfigSelection,
   modelConfigKey,
   getUserSettingsPath,
+  getUserConfigDir,
+  getUserDataDir,
   getProjectSettingsPath,
   getDefaultContextWindow,
   getDefaultAutoCompactWindow,
diff --git a/packages/core/src/session.ts b/packages/core/src/session.ts
index b9252eaa..b54acf48 100644
--- a/packages/core/src/session.ts
+++ b/packages/core/src/session.ts
@@ -30,6 +30,7 @@ import {
 import { McpManager } from "./mcp/mcp-manager";
 import {
   getDefaultAutoCompactWindow,
+  getUserDataDir,
   type McpServerConfig,
   type PermissionScope,
   type PermissionSettings,
@@ -845,7 +846,7 @@ ${agentInstructions}
     return [
       { root: path.join(this.projectRoot, ".deepcode", "skills"), displayRoot: "./.deepcode/skills" },
       { root: path.join(this.projectRoot, ".agents", "skills"), displayRoot: "./.agents/skills" },
-      { root: path.join(homeDir, ".deepcode", "skills"), displayRoot: "~/.deepcode/skills" },
+      { root: path.join(getUserDataDir(), "skills"), displayRoot: "~/.deepcode/skills" },
       { root: path.join(homeDir, ".agents", "skills"), displayRoot: "~/.agents/skills" },
       { root: this.getBundledSkillsRoot(), displayRoot: "bundled:" },
     ];
@@ -2008,7 +2009,7 @@ ${agentInstructions}
     sessionsIndexPath: string;
   } {
     const projectCode = getProjectCode(this.projectRoot);
-    const projectDir = path.join(os.homedir(), ".deepcode", "projects", projectCode);
+    const projectDir = path.join(getUserDataDir(), "projects", projectCode);
     const sessionsIndexPath = path.join(projectDir, "sessions-index.json");
     return { projectCode, projectDir, sessionsIndexPath };
   }
@@ -2400,7 +2401,7 @@ ${agentInstructions}
       return projectInstructions.content;
     }
 
-    return this.readNonEmptyFile(path.join(os.homedir(), ".deepcode", "AGENTS.md"));
+    return this.readNonEmptyFile(path.join(getUserDataDir(), "AGENTS.md"));
   }
 
   private buildSystemMessage(
diff --git a/packages/core/src/settings.ts b/packages/core/src/settings.ts
index da0e2d94..4ed33d80 100644
--- a/packages/core/src/settings.ts
+++ b/packages/core/src/settings.ts
@@ -655,8 +655,24 @@ export const DEFAULT_BASE_URL = "https://api.deepseek.com";
 // Settings file I/O
 // ---------------------------------------------------------------------------
 
+/** User-level config directory. Honors $XDG_CONFIG_HOME/deepcode on Linux; defaults to ~/.deepcode. (#226) */
+export function getUserConfigDir(): string {
+  if (process.platform === "linux" && process.env.XDG_CONFIG_HOME) {
+    return path.join(process.env.XDG_CONFIG_HOME, "deepcode");
+  }
+  return path.join(os.homedir(), ".deepcode");
+}
+
+/** User-level data directory (projects, logs, machine-id). Honors $XDG_DATA_HOME/deepcode on Linux; defaults to ~/.deepcode. (#226) */
+export function getUserDataDir(): string {
+  if (process.platform === "linux" && process.env.XDG_DATA_HOME) {
+    return path.join(process.env.XDG_DATA_HOME, "deepcode");
+  }
+  return path.join(os.homedir(), ".deepcode");
+}
+
 export function getUserSettingsPath(): string {
-  return path.join(os.homedir(), ".deepcode", "settings.json");
+  return path.join(getUserConfigDir(), "settings.json");
 }
 
 export function getProjectSettingsPath(projectRoot: string): string {
diff --git a/packages/core/src/tests/settings-and-notify.test.ts b/packages/core/src/tests/settings-and-notify.test.ts
index 93e8dc29..ebc4f1ef 100644
--- a/packages/core/src/tests/settings-and-notify.test.ts
+++ b/packages/core/src/tests/settings-and-notify.test.ts
@@ -8,9 +8,46 @@ import {
   type NotifySpawn,
 } from "../common/notify";
 import { applyModelConfigSelection, resolveSettings, resolveSettingsSources } from "../settings";
+import * as fs from "fs";
+import * as os from "os";
+import * as path from "path";
+import { getUserConfigDir, getUserDataDir, getUserSettingsPath } from "../settings";
 
 const TEST_PROCESS_ENV = {};
 
+test("getUserConfigDir and getUserDataDir honor XDG env vars on Linux (#226)", () => {
+  const originalPlatform = Object.getOwnPropertyDescriptor(process, "platform");
+  const originalConfig = process.env.XDG_CONFIG_HOME;
+  const originalData = process.env.XDG_DATA_HOME;
+  try {
+    Object.defineProperty(process, "platform", { value: "linux" });
+    process.env.XDG_CONFIG_HOME = "/tmp/xdg-config";
+    process.env.XDG_DATA_HOME = "/tmp/xdg-data";
+    assert.equal(getUserConfigDir(), path.join("/tmp/xdg-config", "deepcode"));
+    assert.equal(getUserDataDir(), path.join("/tmp/xdg-data", "deepcode"));
+    assert.equal(getUserSettingsPath(), path.join("/tmp/xdg-config", "deepcode", "settings.json"));
+
+    delete process.env.XDG_CONFIG_HOME;
+    delete process.env.XDG_DATA_HOME;
+    assert.equal(getUserConfigDir(), path.join(os.homedir(), ".deepcode"));
+    assert.equal(getUserDataDir(), path.join(os.homedir(), ".deepcode"));
+  } finally {
+    if (originalConfig === undefined) {
+      delete process.env.XDG_CONFIG_HOME;
+    } else {
+      process.env.XDG_CONFIG_HOME = originalConfig;
+    }
+    if (originalData === undefined) {
+      delete process.env.XDG_DATA_HOME;
+    } else {
+      process.env.XDG_DATA_HOME = originalData;
+    }
+    if (originalPlatform) {
+      Object.defineProperty(process, "platform", originalPlatform);
+    }
+  }
+});
+
 test("resolveSettings reads top-level thinkingEnabled, notify, and webSearchTool", () => {
   const resolved = resolveSettings(
     {
diff --git a/packages/vscode-ide-companion/src/extension.ts b/packages/vscode-ide-companion/src/extension.ts
index 37243c93..b64791ee 100644
--- a/packages/vscode-ide-companion/src/extension.ts
+++ b/packages/vscode-ide-companion/src/extension.ts
@@ -1,7 +1,6 @@
 import * as vscode from "vscode";
 import * as fs from "fs";
 import * as path from "path";
-import * as os from "os";
 import OpenAI from "openai";
 import MarkdownIt from "markdown-it";
 import type { SessionMessage } from "@vegamo/deepcode-core";
@@ -17,6 +16,7 @@ import {
   type DeepcodingSettings,
   type ReasoningEffort,
   type ResolvedDeepcodingSettings,
+  getUserSettingsPath,
   setShellIfWindows,
 } from "@vegamo/deepcode-core";
 import { getNonce } from "./utils.js";
@@ -438,7 +438,7 @@ export class DeepCodeViewProvider implements vscode.WebviewViewProvider {
 
   private readUserSettings(): DeepcodingSettings | null {
     try {
-      const settingsPath = path.join(os.homedir(), ".deepcode", "settings.json");
+      const settingsPath = getUserSettingsPath();
       if (!fs.existsSync(settingsPath)) {
         return null;
       }