diff --git a/news/changelog-1.9.md b/news/changelog-1.9.md
index f5953cd5088..fe359ba3d8b 100644
--- a/news/changelog-1.9.md
+++ b/news/changelog-1.9.md
@@ -59,3 +59,4 @@ All changes included in 1.9:
 - ([#13402](https://github.com/quarto-dev/quarto-cli/issues/13402)): `nfpm` (<https://nfpm.goreleaser.com/>) is now used to create the `.deb` package, and new `.rpm` package. Both Linux packages are also now built for `x86_64` (`amd64`) and `aarch64` (`arm64`) architectures.
 - ([#13528](https://github.com/quarto-dev/quarto-cli/pull/13528)): Adds support for table specification using nested lists and the `list-table` class.
 - ([#13575](https://github.com/quarto-dev/quarto-cli/pull/13575)): Improve CPU architecture detection/reporting in macOS to allow quarto to run in virtualized environments such as OpenAI's `codex`.
+- ([#13625](https://github.com/quarto-dev/quarto-cli/issues/13625)): Fix Windows file locking error (os error 32) when rendering with `--output-dir` flag. Context cleanup now happens before removing the temporary `.quarto` directory, ensuring file handles are properly closed.
diff --git a/src/command/render/project.ts b/src/command/render/project.ts
index 4e11ac62eb2..6156e9b8508 100644
--- a/src/command/render/project.ts
+++ b/src/command/render/project.ts
@@ -886,13 +886,20 @@ export async function renderProject(
     );
   }
 
-  // in addition to the cleanup above, if forceClean is set, we need to clean up the project scratch dir
-  // entirely. See options.forceClean in render-shared.ts
-  // .quarto is really a fiction created because of `--output-dir` being set on non-project
-  // renders
+  // Clean up synthetic project created for --output-dir
+  // When --output-dir is used without a project file, we create a temporary
+  // project context with a .quarto directory (see render-shared.ts).
+  // After rendering completes, we must remove this directory to avoid leaving
+  // debris in non-project directories (#9745).
   //
-  // cf https://github.com/quarto-dev/quarto-cli/issues/9745#issuecomment-2125951545
+  // Critical ordering for Windows: Close file handles BEFORE removing directory
+  // to avoid "The process cannot access the file because it is being used by
+  // another process" (os error 32) (#13625).
   if (projectRenderConfig.options.forceClean) {
+    // 1. Close all file handles (KV database, temp context, etc.)
+    context.cleanup();
+
+    // 2. Remove the temporary .quarto directory
     const scratchDir = join(projDir, kQuartoScratch);
     if (existsSync(scratchDir)) {
       safeRemoveSync(scratchDir, { recursive: true });
diff --git a/src/command/render/render-shared.ts b/src/command/render/render-shared.ts
index 1783e4a0d44..2affd4004a7 100644
--- a/src/command/render/render-shared.ts
+++ b/src/command/render/render-shared.ts
@@ -48,12 +48,14 @@ export async function render(
   // determine target context/files
   let context = await projectContext(path, nbContext, options);
 
-  // if there is no project parent and an output-dir was passed, then force a project
+  // Create a synthetic project when --output-dir is used without a project file
+  // This creates a temporary .quarto directory to manage the render, which must
+  // be fully cleaned up afterward to avoid leaving debris (see #9745)
   if (!context && options.flags?.outputDir) {
-    // recompute context
     context = await projectContextForDirectory(path, nbContext, options);
 
-    // force clean as --output-dir implies fully overwrite the target
+    // forceClean signals this is a synthetic project that needs full cleanup
+    // including removing the .quarto scratch directory after rendering (#13625)
     options.forceClean = options.flags.clean !== false;
   }
 
diff --git a/tests/docs/render-output-dir/.gitignore b/tests/docs/render-output-dir/.gitignore
new file mode 100644
index 00000000000..ad293093b07
--- /dev/null
+++ b/tests/docs/render-output-dir/.gitignore
@@ -0,0 +1,2 @@
+/.quarto/
+**/*.quarto_ipynb
diff --git a/tests/docs/render-output-dir/test.qmd b/tests/docs/render-output-dir/test.qmd
new file mode 100644
index 00000000000..67f17142538
--- /dev/null
+++ b/tests/docs/render-output-dir/test.qmd
@@ -0,0 +1,6 @@
+---
+title: "Test Output Dir"
+format: html
+---
+
+This is a simple document to test rendering with --output-dir flag.
diff --git a/tests/smoke/render/render-output-dir.test.ts b/tests/smoke/render/render-output-dir.test.ts
new file mode 100644
index 00000000000..22fd04f3fe0
--- /dev/null
+++ b/tests/smoke/render/render-output-dir.test.ts
@@ -0,0 +1,54 @@
+/*
+* render-output-dir.test.ts
+*
+* Test for Windows file locking issue with --output-dir flag
+* Regression test for: https://github.com/quarto-dev/quarto-cli/issues/13625
+*
+* Copyright (C) 2020-2025 Posit Software, PBC
+*
+*/
+import { existsSync, safeRemoveSync } from "../../../src/deno_ral/fs.ts";
+import { docs } from "../../utils.ts";
+import { isWindows } from "../../../src/deno_ral/platform.ts";
+import { fileExists, pathDoNotExists } from "../../verify.ts";
+import { testRender } from "./render.ts";
+import type { Verify } from "../../test.ts";
+
+
+const inputDir = docs("render-output-dir/");
+const quartoDir = ".quarto";
+const outputDir = "output-test-dir";
+
+const cleanupDirs = async () => {
+  if (existsSync(outputDir)) {
+    safeRemoveSync(outputDir, { recursive: true });
+  }
+  if (existsSync(quartoDir)) {
+    safeRemoveSync(quartoDir, { recursive: true });
+  }
+};
+
+const testOutputDirRender = (
+  quartoVerify: Verify,
+  extraArgs: string[] = [],
+) => {
+  testRender(
+    "test.qmd",
+    "html",
+    false,
+    [quartoVerify],
+    {
+      cwd: () => inputDir,
+      setup: cleanupDirs,
+      teardown: cleanupDirs,
+    },
+    ["--output-dir", outputDir, ...extraArgs],
+    outputDir,
+  );
+};
+
+// Test 1: Default behavior (clean=true) - .quarto should be removed
+testOutputDirRender(pathDoNotExists(quartoDir));
+
+// Test 2: With --no-clean flag - .quarto should be preserved
+testOutputDirRender(fileExists(quartoDir), ["--no-clean"]);
diff --git a/tests/utils.ts b/tests/utils.ts
index 66db3d6d3c5..f241be7f4ba 100644
--- a/tests/utils.ts
+++ b/tests/utils.ts
@@ -146,9 +146,13 @@ export function outputForInput(
 
   const outputPath: string = projectRoot && projectOutDir !== undefined
       ? join(projectRoot, projectOutDir, dir, `${stem}.${outputExt}`)
+      : projectOutDir !== undefined
+      ? join(projectOutDir, dir, `${stem}.${outputExt}`)
       : join(dir, `${stem}.${outputExt}`);
   const supportPath: string = projectRoot && projectOutDir !== undefined
     ? join(projectRoot, projectOutDir, dir, `${stem}_files`)
+    : projectOutDir !== undefined
+    ? join(projectOutDir, dir, `${stem}_files`)
     : join(dir, `${stem}_files`);
 
   return {
diff --git a/tests/verify.ts b/tests/verify.ts
index bd8689bec0a..27762371522 100644
--- a/tests/verify.ts
+++ b/tests/verify.ts
@@ -236,7 +236,7 @@ export const fileExists = (file: string): Verify => {
 
 export const pathDoNotExists = (path: string): Verify => {
   return {
-    name: `path ${path} exists`,
+    name: `path ${path} do not exists`,
     verify: (_output: ExecuteOutput[]) => {
       verifyNoPath(path);
       return Promise.resolve();