diff --git a/server/src/__tests__/worktree-config.test.ts b/server/src/__tests__/worktree-config.test.ts
index 42a9955e07..65b5a72a55 100644
--- a/server/src/__tests__/worktree-config.test.ts
+++ b/server/src/__tests__/worktree-config.test.ts
@@ -1,7 +1,7 @@
 import fs from "node:fs/promises";
 import os from "node:os";
 import path from "node:path";
-import { afterEach, describe, expect, it } from "vitest";
+import { afterEach, beforeEach, describe, expect, it } from "vitest";
 import {
   applyRuntimePortSelectionToConfig,
   maybePersistWorktreeRuntimePorts,
@@ -11,6 +11,18 @@ import {
 const ORIGINAL_ENV = { ...process.env };
 const ORIGINAL_CWD = process.cwd();
 
+// The ambient shell can carry real PAPERCLIP_* settings (agent shells export
+// PAPERCLIP_CONFIG pointing at the live default instance). Repair helpers
+// resolve paths from these, so a test that forgets to override one would
+// otherwise rewrite the machine's real config/env files.
+beforeEach(() => {
+  for (const key of Object.keys(process.env)) {
+    if (key.startsWith("PAPERCLIP_")) {
+      delete process.env[key];
+    }
+  }
+});
+
 afterEach(() => {
   process.chdir(ORIGINAL_CWD);
 
@@ -139,6 +151,101 @@ describe("worktree config repair", () => {
     expect(process.env.PAPERCLIP_INSTANCE_ID).toBe("pap-884-ai-commits-component");
   });
 
+  it("never rewrites a main-instance env when ambient worktree flags leak into the process", async () => {
+    const tempRoot = await fs.mkdtemp(path.join(os.tmpdir(), "paperclip-worktree-leak-"));
+    const homeDir = path.join(tempRoot, ".paperclip");
+    const instanceRoot = path.join(homeDir, "instances", "default");
+    const configPath = path.join(instanceRoot, "config.json");
+    const envPath = path.join(instanceRoot, ".env");
+
+    await fs.mkdir(instanceRoot, { recursive: true });
+    const originalConfig = JSON.stringify(buildLegacyConfig(instanceRoot), null, 2) + "\n";
+    await fs.writeFile(configPath, originalConfig, "utf8");
+    const cleanEnv = [
+      "# Paperclip environment variables",
+      "# Generated by `paperclip onboard`",
+      `PAPERCLIP_HOME=${JSON.stringify(homeDir)}`,
+      'PAPERCLIP_INSTANCE_ID="default"',
+      `PAPERCLIP_CONFIG=${JSON.stringify(configPath)}`,
+      "",
+    ].join("\n");
+    await fs.writeFile(envPath, cleanEnv, "utf8");
+
+    process.chdir(tempRoot);
+    process.env.PAPERCLIP_IN_WORKTREE = "true";
+    process.env.PAPERCLIP_WORKTREE_NAME = "PAP-884-ai-commits-component";
+    process.env.PAPERCLIP_HOME = homeDir;
+    process.env.PAPERCLIP_INSTANCE_ID = "default";
+    process.env.PAPERCLIP_CONFIG = configPath;
+    delete process.env.PAPERCLIP_CONTEXT;
+
+    const result = maybeRepairLegacyWorktreeConfigAndEnvFiles();
+
+    expect(result).toEqual({ repairedConfig: false, repairedEnv: false });
+    expect(await fs.readFile(envPath, "utf8")).toBe(cleanEnv);
+    expect(await fs.readFile(configPath, "utf8")).toBe(originalConfig);
+    expect(process.env.PAPERCLIP_HOME).toBe(homeDir);
+    expect(process.env.PAPERCLIP_INSTANCE_ID).toBe("default");
+  });
+
+  it("does not persist runtime ports into a main-instance config when ambient worktree flags leak in", async () => {
+    const tempRoot = await fs.mkdtemp(path.join(os.tmpdir(), "paperclip-worktree-leak-ports-"));
+    const homeDir = path.join(tempRoot, ".paperclip");
+    const instanceRoot = path.join(homeDir, "instances", "default");
+    const configPath = path.join(instanceRoot, "config.json");
+
+    await fs.mkdir(instanceRoot, { recursive: true });
+    await fs.writeFile(configPath, JSON.stringify(buildLegacyConfig(instanceRoot), null, 2) + "\n", "utf8");
+
+    process.chdir(tempRoot);
+    process.env.PAPERCLIP_IN_WORKTREE = "true";
+    process.env.PAPERCLIP_WORKTREE_NAME = "PAP-884-ai-commits-component";
+    process.env.PAPERCLIP_HOME = homeDir;
+    process.env.PAPERCLIP_INSTANCE_ID = "default";
+    process.env.PAPERCLIP_CONFIG = configPath;
+    delete process.env.PORT;
+    delete process.env.DATABASE_URL;
+
+    maybePersistWorktreeRuntimePorts({ serverPort: 3999, databasePort: 54399 });
+
+    const writtenConfig = JSON.parse(await fs.readFile(configPath, "utf8"));
+    expect(writtenConfig.server.port).toBe(3100);
+    expect(writtenConfig.database.embeddedPostgresPort).toBe(54329);
+  });
+
+  it("does not adopt a .paperclip config whose own env does not declare a worktree", async () => {
+    const tempRoot = await fs.mkdtemp(path.join(os.tmpdir(), "paperclip-worktree-unattested-"));
+    const repoRoot = path.join(tempRoot, "repo");
+    const paperclipDir = path.join(repoRoot, ".paperclip");
+    const configPath = path.join(paperclipDir, "config.json");
+    const envPath = path.join(paperclipDir, ".env");
+
+    await fs.mkdir(paperclipDir, { recursive: true });
+    const originalConfig =
+      JSON.stringify(buildLegacyConfig(path.join(tempRoot, "shared")), null, 2) + "\n";
+    await fs.writeFile(configPath, originalConfig, "utf8");
+    const nonWorktreeEnv = [
+      "# Paperclip environment variables",
+      `PAPERCLIP_CONFIG=${JSON.stringify(configPath)}`,
+      "",
+    ].join("\n");
+    await fs.writeFile(envPath, nonWorktreeEnv, "utf8");
+
+    process.chdir(repoRoot);
+    process.env.PAPERCLIP_IN_WORKTREE = "true";
+    process.env.PAPERCLIP_WORKTREE_NAME = "PAP-884-ai-commits-component";
+    process.env.PAPERCLIP_WORKTREES_DIR = path.join(tempRoot, ".paperclip-worktrees");
+    delete process.env.PAPERCLIP_HOME;
+    delete process.env.PAPERCLIP_INSTANCE_ID;
+    delete process.env.PAPERCLIP_CONFIG;
+
+    const result = maybeRepairLegacyWorktreeConfigAndEnvFiles();
+
+    expect(result).toEqual({ repairedConfig: false, repairedEnv: false });
+    expect(await fs.readFile(envPath, "utf8")).toBe(nonWorktreeEnv);
+    expect(await fs.readFile(configPath, "utf8")).toBe(originalConfig);
+  });
+
   it("avoids sibling worktree ports when repairing legacy configs", async () => {
     const tempRoot = await fs.mkdtemp(path.join(os.tmpdir(), "paperclip-worktree-repair-ports-"));
     const worktreeRoot = path.join(tempRoot, "PAP-880-thumbs-capture-for-evals-feature");
@@ -552,6 +659,12 @@ describe("worktree config repair", () => {
       "utf8",
     );
 
+    await fs.writeFile(
+      path.join(paperclipDir, ".env"),
+      ["# Paperclip environment variables", "PAPERCLIP_IN_WORKTREE=true", ""].join("\n"),
+      "utf8",
+    );
+
     process.chdir(worktreeRoot);
     process.env.PAPERCLIP_IN_WORKTREE = "true";
     process.env.PAPERCLIP_WORKTREE_NAME = "PAP-878-create-a-mine-tab-in-inbox";
@@ -636,6 +749,12 @@ describe("worktree config repair", () => {
       "utf8",
     );
 
+    await fs.writeFile(
+      path.join(paperclipDir, ".env"),
+      ["# Paperclip environment variables", "PAPERCLIP_IN_WORKTREE=true", ""].join("\n"),
+      "utf8",
+    );
+
     process.chdir(worktreeRoot);
     process.env.PAPERCLIP_IN_WORKTREE = "true";
     process.env.PAPERCLIP_WORKTREE_NAME = "PAP-125-public-base-url";
diff --git a/server/src/worktree-config.ts b/server/src/worktree-config.ts
index 3c23066421..380bb1b55a 100644
--- a/server/src/worktree-config.ts
+++ b/server/src/worktree-config.ts
@@ -115,6 +115,16 @@ function resolveWorktreeRuntimeContext(
   const configPath = resolvePaperclipConfigPath(overrideConfigPath);
   const envPath = resolvePaperclipEnvPath(configPath);
   const persistedEnv = readEnvEntries(envPath);
+
+  // PAPERCLIP_IN_WORKTREE can leak in from a parent process or a sourced env
+  // file while config resolution still points at a non-worktree target (for
+  // example the default instance under <home>/instances/default). Only adopt
+  // a target as a worktree when its config sits in a `<root>/.paperclip/`
+  // layout and its own persisted env already declares it a worktree;
+  // otherwise the repair would rewrite main-instance config and env files.
+  if (path.basename(path.dirname(configPath)) !== ".paperclip") return null;
+  if (persistedEnv.PAPERCLIP_IN_WORKTREE !== "true") return null;
+
   const persistedConfigPath = nonEmpty(persistedEnv.PAPERCLIP_CONFIG);
   const persistedConfigLooksStale =
     persistedConfigPath !== null &&