diff --git a/packages/coding-agent/CHANGELOG.md b/packages/coding-agent/CHANGELOG.md
index e4d966d52..fb3c3ad48 100644
--- a/packages/coding-agent/CHANGELOG.md
+++ b/packages/coding-agent/CHANGELOG.md
@@ -14,6 +14,7 @@
 
 - Fixed X11 clipboard text being misidentified as an image when the clipboard owner accepts unadvertised image targets ([#9786](https://github.com/earendil-works/pi/issues/9786)).
 - Prevented managed git packages from automatically installing Pi peer dependencies and added warnings for extension packages that list host-provided modules in `dependencies` ([#9863](https://github.com/earendil-works/pi/issues/9863)).
+- Fixed pinned git extensions loaded with `-e` continuing to use the first downloaded commit after the ref changes ([#9982](https://github.com/earendil-works/pi/issues/9982)).
 
 ## [0.87.1] - 2026-09-22
 
diff --git a/packages/coding-agent/src/core/package-manager.ts b/packages/coding-agent/src/core/package-manager.ts
index eb6f47825..be42365a9 100644
--- a/packages/coding-agent/src/core/package-manager.ts
+++ b/packages/coding-agent/src/core/package-manager.ts
@@ -2123,7 +2123,8 @@ export class DefaultPackageManager implements PackageManager {
 
 	private getGitInstallPath(source: GitSource, scope: SourceScope): string {
 		if (scope === "temporary") {
-			return this.getTemporaryDir(`git-${source.host}`, source.path);
+			// Include the ref in the hash so each pinned ref gets its own checkout.
+			return this.getTemporaryDir(`git-${source.host}`, source.path, source.ref);
 		}
 		const installRoot = this.getGitInstallRoot(scope);
 		if (!installRoot) {
@@ -2143,10 +2144,10 @@ export class DefaultPackageManager implements PackageManager {
 		return join(this.agentDir, "git");
 	}
 
-	private getTemporaryDir(prefix: string, suffix?: string): string {
+	private getTemporaryDir(prefix: string, suffix?: string, ref?: string): string {
 		const root = this.resolveManagedPath(getExtensionTempFolder(this.agentDir), prefix);
 		const hash = createHash("sha256")
-			.update(`${prefix}-${suffix ?? ""}`)
+			.update(`${prefix}-${suffix ?? ""}${ref ? `@${ref}` : ""}`)
 			.digest("hex")
 			.slice(0, 8);
 		return this.resolveManagedPath(root, hash, suffix ?? "");
diff --git a/packages/coding-agent/test/package-manager.test.ts b/packages/coding-agent/test/package-manager.test.ts
index c93099b81..07cdc9d60 100644
--- a/packages/coding-agent/test/package-manager.test.ts
+++ b/packages/coding-agent/test/package-manager.test.ts
@@ -2615,6 +2615,35 @@ export default function(api) { api.registerTool({ name: "test", description: "te
 			expect(refreshTemporaryGitSourceSpy).not.toHaveBeenCalled();
 		});
 
+		// https://github.com/earendil-works/pi/issues/9982
+		it("should load a new checkout when a pinned temporary git source changes ref", async () => {
+			const managerWithInternals = packageManager as unknown as PackageManagerInternals;
+			const oldSource = "git:github.com/example/repo@aaaaaaa";
+			const newSource = "git:github.com/example/repo@bbbbbbb";
+			const oldParsed = managerWithInternals.parseSource(oldSource);
+			const newParsed = managerWithInternals.parseSource(newSource);
+			if (oldParsed.type !== "git" || newParsed.type !== "git") {
+				throw new Error("Expected git sources");
+			}
+
+			const oldPath = managerWithInternals.getGitInstallPath(oldParsed, "temporary");
+			mkdirSync(join(oldPath, "extensions"), { recursive: true });
+			writeFileSync(join(oldPath, "extensions", "old.ts"), "export default function() {};");
+
+			const installParsedSourceSpy = vi
+				.spyOn(packageManager as any, "installParsedSource")
+				.mockImplementation(async () => {
+					const newPath = managerWithInternals.getGitInstallPath(newParsed, "temporary");
+					mkdirSync(join(newPath, "extensions"), { recursive: true });
+					writeFileSync(join(newPath, "extensions", "new.ts"), "export default function() {};");
+				});
+
+			const result = await packageManager.resolveExtensionSources([newSource], { temporary: true });
+			expect(installParsedSourceSpy).toHaveBeenCalledTimes(1);
+			expect(result.extensions.some((r) => pathEndsWith(r.path, "extensions/new.ts") && r.enabled)).toBe(true);
+			expect(result.extensions.some((r) => pathEndsWith(r.path, "extensions/old.ts"))).toBe(false);
+		});
+
 		it("should not run npm view during resolve for installed unpinned packages", async () => {
 			process.env.PI_OFFLINE = "1";
 			const installedPath = join(tempDir, ".pi", "npm", "node_modules", "example");