diff --git a/news/changelog-1.7.md b/news/changelog-1.7.md
index 8554c5d4e16..9578926bd0c 100644
--- a/news/changelog-1.7.md
+++ b/news/changelog-1.7.md
@@ -162,6 +162,10 @@ All changes included in 1.7:
 
 - ([#12366](https://github.com/quarto-dev/quarto-cli/pull/12366)): Added Bulgarian translation for Quarto UI text (credit: @sakelariev)
 
+## `quarto publish`
+
+- ([#9929](https://github.com/quarto-dev/quarto-cli/issues/9929)): `quarto publish gh-pages` will now clean previous worktree directory leftover from previous deploys.
+
 ## Other Fixes and Improvements
 
 - A new folder `quarto-session-temp` can be created in `.quarto` to store temporary files created by Quarto during a rendering. Reminder: `.quarto` is for internal use of Quarto and should not be versioned (thus added to `.gitignore`).
diff --git a/src/publish/gh-pages/gh-pages.ts b/src/publish/gh-pages/gh-pages.ts
index 3644aa22794..019faf8ab9d 100644
--- a/src/publish/gh-pages/gh-pages.ts
+++ b/src/publish/gh-pages/gh-pages.ts
@@ -4,7 +4,7 @@
  * Copyright (C) 2020-2022 Posit Software, PBC
  */
 
-import { info } from "../../deno_ral/log.ts";
+import { debug, info } from "../../deno_ral/log.ts";
 import { dirname, join, relative } from "../../deno_ral/path.ts";
 import { copy } from "../../deno_ral/fs.ts";
 import * as colors from "fmt/colors";
@@ -33,6 +33,8 @@ import {
   gitHubContextForPublish,
   verifyContext,
 } from "../common/git.ts";
+import { createTempContext } from "../../core/temp.ts";
+import { projectScratchPath } from "../../project/project-scratch.ts";
 
 export const kGhpages = "gh-pages";
 const kGhpagesDescription = "GitHub Pages";
@@ -189,12 +191,35 @@ async function publish(
     type === "site" ? target?.url : undefined,
   );
 
+  const kPublishWorktreeDir = "quarto-publish-worktree-";
   // allocate worktree dir
-  const tempDir = Deno.makeTempDirSync({ dir: input });
+  const temp = createTempContext(
+    { prefix: kPublishWorktreeDir, dir: projectScratchPath(input) },
+  );
+  const tempDir = temp.baseDir;
   removeIfExists(tempDir);
 
-  const deployId = shortUuid();
+  // cleaning up leftover by listing folder with prefix .quarto-publish-worktree- and calling git worktree rm on them
+  const worktreeDir = Deno.readDirSync(projectScratchPath(input));
+  for (const entry of worktreeDir) {
+    if (
+      entry.isDirectory && entry.name.startsWith(kPublishWorktreeDir)
+    ) {
+      debug(
+        `Cleaning up leftover worktree folder ${entry.name} from past deploys`,
+      );
+      const worktreePath = join(projectScratchPath(input), entry.name);
+      await execProcess({
+        cmd: ["git", "worktree", "remove", worktreePath],
+        cwd: projectScratchPath(input),
+      });
+      removeIfExists(worktreePath);
+    }
+  }
 
+  // create worktree and deploy from it
+  const deployId = shortUuid();
+  debug(`Deploying from worktree ${tempDir} with deployId ${deployId}`);
   await withWorktree(input, relative(input, tempDir), async () => {
     // copy output to tempdir and add .nojekyll (include deployId
     // in .nojekyll so we can poll for completed deployment)
@@ -209,6 +234,7 @@ async function publish(
       ["push", "--force", "origin", "HEAD:gh-pages"],
     ]);
   });
+  temp.cleanup();
   info("");
 
   // if this is the creation of gh-pages AND this is a user home/default site