diff --git a/cli/src/__tests__/agent-jwt-env.test.ts b/cli/src/__tests__/agent-jwt-env.test.ts
index 40bb1554..baf5db51 100644
--- a/cli/src/__tests__/agent-jwt-env.test.ts
+++ b/cli/src/__tests__/agent-jwt-env.test.ts
@@ -4,7 +4,9 @@ import path from "node:path";
 import { afterEach, beforeEach, describe, expect, it } from "vitest";
 import {
   ensureAgentJwtSecret,
+  mergePaperclipEnvEntries,
   readAgentJwtSecretFromEnv,
+  readPaperclipEnvEntries,
   resolveAgentJwtEnvFile,
 } from "../config/env.js";
 import { agentJwtSecretCheck } from "../checks/agent-jwt-secret-check.js";
@@ -58,4 +60,20 @@ describe("agent jwt env helpers", () => {
     const result = agentJwtSecretCheck(configPath);
     expect(result.status).toBe("pass");
   });
+
+  it("quotes hash-prefixed env values so dotenv round-trips them", () => {
+    const configPath = tempConfigPath();
+    const envPath = resolveAgentJwtEnvFile(configPath);
+
+    mergePaperclipEnvEntries(
+      {
+        PAPERCLIP_WORKTREE_COLOR: "#439edb",
+      },
+      envPath,
+    );
+
+    const contents = fs.readFileSync(envPath, "utf-8");
+    expect(contents).toContain('PAPERCLIP_WORKTREE_COLOR="#439edb"');
+    expect(readPaperclipEnvEntries(envPath).PAPERCLIP_WORKTREE_COLOR).toBe("#439edb");
+  });
 });
diff --git a/cli/src/__tests__/worktree.test.ts b/cli/src/__tests__/worktree.test.ts
index b6e2eb47..a8333ba5 100644
--- a/cli/src/__tests__/worktree.test.ts
+++ b/cli/src/__tests__/worktree.test.ts
@@ -294,7 +294,7 @@ describe("worktree helpers", () => {
       const envContents = fs.readFileSync(envPath, "utf8");
       expect(envContents).toContain("PAPERCLIP_AGENT_JWT_SECRET=worktree-shared-secret");
       expect(envContents).toContain("PAPERCLIP_WORKTREE_NAME=repo");
-      expect(envContents).toMatch(/PAPERCLIP_WORKTREE_COLOR=#[0-9a-f]{6}/);
+      expect(envContents).toMatch(/PAPERCLIP_WORKTREE_COLOR=\"#[0-9a-f]{6}\"/);
     } finally {
       process.chdir(originalCwd);
       if (originalJwtSecret === undefined) {
diff --git a/cli/src/config/env.ts b/cli/src/config/env.ts
index 4bc8f16e..a7266ea2 100644
--- a/cli/src/config/env.ts
+++ b/cli/src/config/env.ts
@@ -22,11 +22,18 @@ function parseEnvFile(contents: string) {
   }
 }
 
+function formatEnvValue(value: string): string {
+  if (/^[A-Za-z0-9_./:@-]+$/.test(value)) {
+    return value;
+  }
+  return JSON.stringify(value);
+}
+
 function renderEnvFile(entries: Record<string, string>) {
   const lines = [
     "# Paperclip environment variables",
     "# Generated by Paperclip CLI commands",
-    ...Object.entries(entries).map(([key, value]) => `${key}=${value}`),
+    ...Object.entries(entries).map(([key, value]) => `${key}=${formatEnvValue(value)}`),
     "",
   ];
   return lines.join("\n");