diff --git a/crates/uv-virtualenv/src/virtualenv.rs b/crates/uv-virtualenv/src/virtualenv.rs
index 2227b71b9..5fa77034e 100644
--- a/crates/uv-virtualenv/src/virtualenv.rs
+++ b/crates/uv-virtualenv/src/virtualenv.rs
@@ -10,7 +10,7 @@ use fs_err as fs;
 use fs_err::File;
 use itertools::Itertools;
 use owo_colors::OwoColorize;
-use tracing::debug;
+use tracing::{debug, trace};
 
 use uv_configuration::PreviewMode;
 use uv_fs::{CWD, Simplified, cachedir};
@@ -85,6 +85,18 @@ pub(crate) fn create(
                 format!("File exists at `{}`", location.user_display()),
             )));
         }
+        Ok(metadata)
+            if metadata.is_dir()
+                && location
+                    .read_dir()
+                    .is_ok_and(|mut dir| dir.next().is_none()) =>
+        {
+            // If it's an empty directory, we can proceed
+            trace!(
+                "Using empty directory at `{}` for virtual environment",
+                location.user_display()
+            );
+        }
         Ok(metadata) if metadata.is_dir() => {
             let name = if uv_fs::is_virtualenv_base(location) {
                 "virtual environment"
@@ -100,13 +112,6 @@ pub(crate) fn create(
                     remove_virtualenv(location)?;
                     fs::create_dir_all(location)?;
                 }
-                OnExisting::Fail
-                    if location
-                        .read_dir()
-                        .is_ok_and(|mut dir| dir.next().is_none()) =>
-                {
-                    debug!("Ignoring empty directory");
-                }
                 OnExisting::Fail => {
                     match confirm_clear(location, name)? {
                         Some(true) => {
diff --git a/crates/uv/tests/it/sync.rs b/crates/uv/tests/it/sync.rs
index 9905c8a65..a5ea6aded 100644
--- a/crates/uv/tests/it/sync.rs
+++ b/crates/uv/tests/it/sync.rs
@@ -11393,3 +11393,49 @@ fn sync_config_settings_package() -> Result<()> {
 
     Ok(())
 }
+
+/// Ensure that when we sync to an empty virtual environment directory, we don't attempt to remove
+/// it, which breaks Docker volume mounts.
+#[test]
+#[cfg(unix)]
+fn sync_does_not_remove_empty_virtual_environment_directory() -> Result<()> {
+    use std::os::unix::fs::PermissionsExt;
+
+    let context = TestContext::new_with_versions(&["3.12"]);
+
+    let project_dir = context.temp_dir.child("project");
+    fs_err::create_dir(&project_dir)?;
+
+    let pyproject_toml = project_dir.child("pyproject.toml");
+    pyproject_toml.write_str(
+        r#"
+        [project]
+        name = "project"
+        version = "0.1.0"
+        requires-python = ">=3.12"
+        dependencies = ["iniconfig"]
+        "#,
+    )?;
+
+    let venv_dir = project_dir.child(".venv");
+    fs_err::create_dir(&venv_dir)?;
+
+    // Ensure the parent is read-only, to prevent deletion of the virtual environment
+    fs_err::set_permissions(&project_dir, std::fs::Permissions::from_mode(0o555))?;
+
+    // Note we do _not_ fail to create the virtual environment — we fail later when writing to the
+    // project directory
+    uv_snapshot!(context.filters(), context.sync().current_dir(&project_dir), @r"
+    success: false
+    exit_code: 2
+    ----- stdout -----
+
+    ----- stderr -----
+    Using CPython 3.12.[X] interpreter at: [PYTHON-3.12]
+    Creating virtual environment at: .venv
+    Resolved 2 packages in [TIME]
+    error: failed to write to file `[TEMP_DIR]/project/uv.lock`: Permission denied (os error 13)
+    ");
+
+    Ok(())
+}