diff --git a/src/main/core/paths.ts b/src/main/core/paths.ts
index c1d67a7ec..a630e9e57 100644
--- a/src/main/core/paths.ts
+++ b/src/main/core/paths.ts
@@ -96,6 +96,37 @@ export function windowsStorageRoots(
   };
 }
 
+export interface LinuxStorageHomes {
+  readonly config: string;
+  readonly data: string;
+  readonly cache: string;
+  readonly state: string;
+}
+
+/** Resolve the Flatpak layout beneath the sandbox-provided XDG homes. */
+export function linuxStorageRoots(
+  homes: LinuxStorageHomes,
+): ApplicationStorageRoots {
+  for (const [name, root] of Object.entries(homes)) {
+    if (!path.posix.isAbsolute(root)) {
+      throw new Error(`Linux ${name} home must be absolute`);
+    }
+  }
+
+  const config = path.posix.join(homes.config, "gwonmac");
+  const data = path.posix.join(homes.data, "gwonmac");
+  const cache = path.posix.join(homes.cache, "gwonmac");
+  const state = path.posix.join(homes.state, "gwonmac");
+  return {
+    config,
+    data,
+    cache,
+    state,
+    logs: path.posix.join(state, "logs"),
+    sessions: path.posix.join(data, "sessions"),
+  };
+}
+
 export function gamePaths(storage: ApplicationStorageRoots): GamePaths {
   const game = path.join(storage.cache, "game");
   const artifacts = path.join(game, "artifacts");
diff --git a/src/main/main.ts b/src/main/main.ts
index 5a4a8fce7..1547802eb 100644
--- a/src/main/main.ts
+++ b/src/main/main.ts
@@ -81,6 +81,7 @@ import { sweepOrphanDirectories } from "./core/atomic-file.js";
 import {
   colocatedStorageRoots,
   documentDirectories,
+  linuxStorageRoots,
   windowsStorageRoots,
 } from "./core/paths.js";
 import { gamePaths } from "./paths.js";
@@ -200,12 +201,23 @@ const explicitUserData = app.commandLine.hasSwitch("user-data-dir");
 if (!explicitUserData && process.platform === "darwin") {
   app.setPath("userData", path.join(app.getPath("appData"), "Guild Wars"));
 }
+const linuxFlatpak = process.platform === "linux"
+  && process.env.FLATPAK_ID === DISTRIBUTION_CHANNEL_CONFIG.release.bundleId;
 const applicationStorageRoots = explicitUserData
   ? colocatedStorageRoots(app.getPath("userData"))
   : windowsNativeHost
     ? windowsStorageRoots(windowsNativeHost.localAppData())
+    : linuxFlatpak
+      ? linuxStorageRoots({
+        config: process.env.XDG_CONFIG_HOME ?? app.getPath("appData"),
+        data: process.env.XDG_DATA_HOME ?? app.getPath("appData"),
+        cache:
+          process.env.XDG_CACHE_HOME ?? path.join(app.getPath("home"), ".cache"),
+        state: process.env.XDG_STATE_HOME
+          ?? path.join(process.env.XDG_DATA_HOME ?? app.getPath("appData"), "state"),
+      })
     : colocatedStorageRoots(app.getPath("userData"));
-if (!explicitUserData && process.platform === "win32") {
+if (!explicitUserData && (process.platform === "win32" || linuxFlatpak)) {
   app.setPath("userData", applicationStorageRoots.sessions);
   app.setPath("sessionData", applicationStorageRoots.sessions);
 }
diff --git a/tests/unit/paths.test.ts b/tests/unit/paths.test.ts
index b43c28045..087365e9a 100644
--- a/tests/unit/paths.test.ts
+++ b/tests/unit/paths.test.ts
@@ -7,6 +7,7 @@ import {
   diagnosticFramesPath,
   documentDirectories,
   gamePaths,
+  linuxStorageRoots,
   multiProfilePaths,
   nativeExecutableName,
   unpackedPath,
@@ -223,4 +224,29 @@ describe("resolved profile paths", () => {
         "C:\\Users\\Player\\AppData\\Local\\Guild Wars Reforged\\data\\sessions",
     });
   });
+
+  it("pins the Flatpak layout beneath sandbox-provided XDG homes", () => {
+    assert.deepEqual(linuxStorageRoots({
+      config: "/var/config",
+      data: "/var/data",
+      cache: "/var/cache",
+      state: "/var/state",
+    }), {
+      config: "/var/config/gwonmac",
+      data: "/var/data/gwonmac",
+      cache: "/var/cache/gwonmac",
+      state: "/var/state/gwonmac",
+      logs: "/var/state/gwonmac/logs",
+      sessions: "/var/data/gwonmac/sessions",
+    });
+  });
+
+  it("refuses relative Linux XDG homes", () => {
+    assert.throws(() => linuxStorageRoots({
+      config: "config",
+      data: "/var/data",
+      cache: "/var/cache",
+      state: "/var/state",
+    }), /Linux config home must be absolute/);
+  });
 });