diff --git a/gix/src/clone/mod.rs b/gix/src/clone/mod.rs
index c3d50ad3d9..7ca001f8d9 100644
--- a/gix/src/clone/mod.rs
+++ b/gix/src/clone/mod.rs
@@ -102,7 +102,10 @@ impl PrepareFetch {
         mut create_opts: crate::create::Options,
         open_opts: crate::open::Options,
     ) -> Result<Self, Error> {
-        create_opts.destination_must_be_empty = true;
+        if create_opts.destination_must_be_empty.is_none() {
+            create_opts.destination_must_be_empty = Some(true);
+        }
+
         let mut repo = crate::ThreadSafeRepository::init_opts(path, kind, create_opts, open_opts)?.to_thread_local();
         url.canonicalize(repo.options.current_dir_or_empty())
             .map_err(|err| Error::CanonicalizeUrl {
diff --git a/gix/src/create.rs b/gix/src/create.rs
index d6395edaa4..b04349d375 100644
--- a/gix/src/create.rs
+++ b/gix/src/create.rs
@@ -113,7 +113,7 @@ pub struct Options {
     /// If true, and the kind of repository to create has a worktree, then the destination directory must be empty.
     ///
     /// By default repos with worktree can be initialized into a non-empty repository as long as there is no `.git` directory.
-    pub destination_must_be_empty: bool,
+    pub destination_must_be_empty: Option<bool>,
     /// If set, use these filesystem capabilities to populate the respective git-config fields.
     /// If `None`, the directory will be probed.
     pub fs_capabilities: Option<gix_fs::Capabilities>,
@@ -135,7 +135,7 @@ pub fn into(
     let mut dot_git = directory.into();
     let bare = matches!(kind, Kind::Bare);
 
-    if bare || destination_must_be_empty {
+    if bare || destination_must_be_empty.unwrap_or(false) {
         let num_entries_in_dot_git = fs::read_dir(&dot_git)
             .or_else(|err| {
                 if err.kind() == std::io::ErrorKind::NotFound {
diff --git a/gix/tests/gix/clone.rs b/gix/tests/gix/clone.rs
index c24ae33f3d..25d03f6b38 100644
--- a/gix/tests/gix/clone.rs
+++ b/gix/tests/gix/clone.rs
@@ -550,6 +550,36 @@ mod blocking_io {
         assure_index_entries_on_disk(&index, repo.workdir().expect("non-bare"));
         Ok(())
     }
+
+    #[test]
+    fn fetch_and_checkout_into_non_empty_directory() -> crate::Result {
+        let tmp = gix_testtools::tempfile::TempDir::new()?;
+        let existing_path = tmp.path().join("existing.txt");
+        let existing_content = b"I was here before you";
+        std::fs::write(&existing_path, existing_content)?;
+
+        let mut prepare = gix::clone::PrepareFetch::new(
+            remote::repo("base").path(),
+            tmp.path(),
+            gix::create::Kind::WithWorktree,
+            gix::create::Options {
+                destination_must_be_empty: Some(false),
+                ..Default::default()
+            },
+            restricted(),
+        )?;
+        let (mut checkout, _out) =
+            prepare.fetch_then_checkout(gix::progress::Discard, &std::sync::atomic::AtomicBool::default())?;
+        let (repo, _) = checkout.main_worktree(gix::progress::Discard, &std::sync::atomic::AtomicBool::default())?;
+
+        let index = repo.index()?;
+        assert_eq!(index.entries().len(), 1, "All entries are known as per HEAD tree");
+        assure_index_entries_on_disk(&index, repo.workdir().expect("non-bare"));
+
+        assert_eq!(std::fs::read(&existing_path)?, existing_content);
+        Ok(())
+    }
+
     #[test]
     fn fetch_and_checkout_specific_ref() -> crate::Result {
         let tmp = gix_testtools::tempfile::TempDir::new()?;
@@ -800,6 +830,25 @@ fn clone_and_destination_must_be_empty() -> crate::Result {
     Ok(())
 }
 
+#[test]
+fn clone_with_worktree_and_destination_must_be_empty() -> crate::Result {
+    let tmp = gix_testtools::tempfile::TempDir::new()?;
+    std::fs::write(tmp.path().join("file"), b"hello")?;
+    match gix::clone::PrepareFetch::new(
+        remote::repo("base").path(),
+        tmp.path(),
+        gix::create::Kind::WithWorktree,
+        Default::default(),
+        restricted(),
+    ) {
+        Ok(_) => unreachable!("this should fail as the directory isn't empty"),
+        Err(err) => assert!(err
+            .to_string()
+            .starts_with("Refusing to initialize the non-empty directory as ")),
+    }
+    Ok(())
+}
+
 #[test]
 fn clone_bare_into_empty_directory_and_early_drop() -> crate::Result {
     let tmp = gix_testtools::tempfile::TempDir::new()?;
diff --git a/gix/tests/gix/init.rs b/gix/tests/gix/init.rs
index 09e54c0a9d..be8fe7ff43 100644
--- a/gix/tests/gix/init.rs
+++ b/gix/tests/gix/init.rs
@@ -170,7 +170,7 @@ mod non_bare {
             tmp.path(),
             gix::create::Kind::WithWorktree,
             gix::create::Options {
-                destination_must_be_empty: true,
+                destination_must_be_empty: Some(true),
                 ..Default::default()
             },
             gix::open::Options::isolated(),