diff --git a/doc/DEVELOPING.md b/doc/DEVELOPING.md
index 7958ffd19cc..225ae9ffead 100644
--- a/doc/DEVELOPING.md
+++ b/doc/DEVELOPING.md
@@ -222,6 +222,8 @@ That repo-local env also sets:
 - `PAPERCLIP_WORKTREE_COLOR=<hex-color>`
 
 The server/UI use those values for worktree-specific branding such as the top banner and dynamically colored favicon.
+Authenticated worktree servers also use the `PAPERCLIP_INSTANCE_ID` value to scope Better Auth cookie names.
+Browser cookies are shared by host rather than port, so this prevents logging into one `127.0.0.1:<port>` worktree from replacing another worktree server's session cookie.
 
 Print shell exports explicitly when needed:
 
diff --git a/server/src/__tests__/better-auth.test.ts b/server/src/__tests__/better-auth.test.ts
new file mode 100644
index 00000000000..79bfa3e75bb
--- /dev/null
+++ b/server/src/__tests__/better-auth.test.ts
@@ -0,0 +1,43 @@
+import { afterEach, describe, expect, it } from "vitest";
+import type { BetterAuthOptions } from "better-auth";
+import { getCookies } from "better-auth/cookies";
+import {
+  buildBetterAuthAdvancedOptions,
+  deriveAuthCookiePrefix,
+} from "../auth/better-auth.js";
+
+const ORIGINAL_INSTANCE_ID = process.env.PAPERCLIP_INSTANCE_ID;
+
+afterEach(() => {
+  if (ORIGINAL_INSTANCE_ID === undefined) delete process.env.PAPERCLIP_INSTANCE_ID;
+  else process.env.PAPERCLIP_INSTANCE_ID = ORIGINAL_INSTANCE_ID;
+});
+
+describe("Better Auth cookie scoping", () => {
+  it("derives an instance-scoped cookie prefix", () => {
+    expect(deriveAuthCookiePrefix("default")).toBe("paperclip-default");
+    expect(deriveAuthCookiePrefix("PAP-1601-worktree")).toBe("paperclip-PAP-1601-worktree");
+  });
+
+  it("uses PAPERCLIP_INSTANCE_ID for the Better Auth cookie prefix", () => {
+    process.env.PAPERCLIP_INSTANCE_ID = "sat-worktree";
+
+    const advanced = buildBetterAuthAdvancedOptions({ disableSecureCookies: false });
+
+    expect(advanced).toEqual({
+      cookiePrefix: "paperclip-sat-worktree",
+    });
+    expect(getCookies({ advanced } as BetterAuthOptions).sessionToken.name).toBe(
+      "paperclip-sat-worktree.session_token",
+    );
+  });
+
+  it("keeps local http auth cookies non-secure while preserving the scoped prefix", () => {
+    process.env.PAPERCLIP_INSTANCE_ID = "pap-worktree";
+
+    expect(buildBetterAuthAdvancedOptions({ disableSecureCookies: true })).toEqual({
+      cookiePrefix: "paperclip-pap-worktree",
+      useSecureCookies: false,
+    });
+  });
+});
diff --git a/server/src/auth/better-auth.ts b/server/src/auth/better-auth.ts
index 881c3072ca5..402dad52036 100644
--- a/server/src/auth/better-auth.ts
+++ b/server/src/auth/better-auth.ts
@@ -11,6 +11,7 @@ import {
   authVerifications,
 } from "@paperclipai/db";
 import type { Config } from "../config.js";
+import { resolvePaperclipInstanceId } from "../home-paths.js";
 
 export type BetterAuthSessionUser = {
   id: string;
@@ -25,6 +26,24 @@ export type BetterAuthSessionResult = {
 
 type BetterAuthInstance = ReturnType<typeof betterAuth>;
 
+const AUTH_COOKIE_PREFIX_FALLBACK = "default";
+const AUTH_COOKIE_PREFIX_INVALID_SEGMENTS_RE = /[^a-zA-Z0-9_-]+/g;
+
+export function deriveAuthCookiePrefix(instanceId = resolvePaperclipInstanceId()): string {
+  const scopedInstanceId = instanceId
+    .trim()
+    .replace(AUTH_COOKIE_PREFIX_INVALID_SEGMENTS_RE, "-")
+    .replace(/^-+|-+$/g, "") || AUTH_COOKIE_PREFIX_FALLBACK;
+  return `paperclip-${scopedInstanceId}`;
+}
+
+export function buildBetterAuthAdvancedOptions(input: { disableSecureCookies: boolean }) {
+  return {
+    cookiePrefix: deriveAuthCookiePrefix(),
+    ...(input.disableSecureCookies ? { useSecureCookies: false } : {}),
+  };
+}
+
 function headersFromNodeHeaders(rawHeaders: IncomingHttpHeaders): Headers {
   const headers = new Headers();
   for (const [key, raw] of Object.entries(rawHeaders)) {
@@ -97,7 +116,7 @@ export function createBetterAuthInstance(db: Db, config: Config, trustedOrigins?
       requireEmailVerification: false,
       disableSignUp: config.authDisableSignUp,
     },
-    ...(isHttpOnly ? { advanced: { useSecureCookies: false } } : {}),
+    advanced: buildBetterAuthAdvancedOptions({ disableSecureCookies: isHttpOnly }),
   };
 
   if (!baseUrl) {