diff --git a/packages/coding-agent/src/config/settings.ts b/packages/coding-agent/src/config/settings.ts
index 23ae1d0c6..cab46a635 100644
--- a/packages/coding-agent/src/config/settings.ts
+++ b/packages/coding-agent/src/config/settings.ts
@@ -458,6 +458,7 @@ export class Settings {
 			inMemory: !this.#persist,
 		});
 		cloned.#storage = this.#storage;
+		cloned.#configPath = this.#configPath;
 		cloned.#global = structuredClone(this.#global);
 		cloned.#project = this.#persist ? await cloned.#loadProjectSettings() : structuredClone(this.#project);
 		cloned.#configFiles = [...this.#configFiles];
diff --git a/packages/coding-agent/test/settings-manager.test.ts b/packages/coding-agent/test/settings-manager.test.ts
index f721c5640..daf6e15a0 100644
--- a/packages/coding-agent/test/settings-manager.test.ts
+++ b/packages/coding-agent/test/settings-manager.test.ts
@@ -87,6 +87,21 @@ describe("Settings", () => {
 			expect(await Bun.file(getConfigPath()).exists()).toBe(false);
 		});
 
+		it("clones the selected config.yaml path for persisted settings", async () => {
+			const yamlConfigPath = path.join(agentDir, "config.yaml");
+			await Bun.write(yamlConfigPath, YAML.stringify({ setupVersion: 1 }, null, 2));
+
+			const settings = await Settings.init({ cwd: projectDir, agentDir });
+			const cloned = await settings.cloneForCwd(tempDir.join("other-project"));
+
+			cloned.set("setupVersion", 2);
+			await cloned.flush();
+
+			const savedSettings = YAML.parse(await Bun.file(yamlConfigPath).text()) as Record<string, unknown>;
+			expect(savedSettings.setupVersion).toBe(2);
+			expect(await Bun.file(getConfigPath()).exists()).toBe(false);
+		});
+
 		it("creates config.yml for new persisted settings when no main config exists", async () => {
 			const yamlConfigPath = path.join(agentDir, "config.yaml");