diff --git a/crates/uv/src/commands/project/mod.rs b/crates/uv/src/commands/project/mod.rs
index 56907f74e83fd..8297d2e8991d2 100644
--- a/crates/uv/src/commands/project/mod.rs
+++ b/crates/uv/src/commands/project/mod.rs
@@ -120,6 +120,9 @@ pub(crate) enum ProjectError {
     #[error("Environment marker is empty")]
     EmptyEnvironment,
 
+    #[error("Project virtual environment directory `{0}` cannot be used because it has existing, non-virtual environment content")]
+    InvalidProjectEnvironmentDir(PathBuf),
+
     #[error("Failed to parse `pyproject.toml`")]
     TomlParse(#[source] toml::de::Error),
 
@@ -488,6 +491,14 @@ pub(crate) async fn get_or_init_environment(
         FoundInterpreter::Interpreter(interpreter) => {
             let venv = workspace.venv();
 
+            // Before deleting the target directory, we confirm that it is either (1) a virtual
+            // environment or (2) an empty directory.
+            if PythonEnvironment::from_root(&venv, cache).is_err()
+                && fs_err::read_dir(&venv).is_ok_and(|mut dir| dir.next().is_some())
+            {
+                return Err(ProjectError::InvalidProjectEnvironmentDir(venv));
+            }
+
             // Remove the existing virtual environment if it doesn't meet the requirements.
             match fs_err::remove_dir_all(&venv) {
                 Ok(()) => {
diff --git a/crates/uv/tests/sync.rs b/crates/uv/tests/sync.rs
index 7fcc80c3d8bb4..ab31ecb58fb75 100644
--- a/crates/uv/tests/sync.rs
+++ b/crates/uv/tests/sync.rs
@@ -1613,7 +1613,7 @@ fn convert_to_package() -> Result<()> {
 
 #[test]
 fn sync_custom_environment_path() -> Result<()> {
-    let mut context = TestContext::new("3.12");
+    let mut context = TestContext::new_with_versions(&["3.11", "3.12"]);
 
     let pyproject_toml = context.temp_dir.child("pyproject.toml");
     pyproject_toml.write_str(
@@ -1633,6 +1633,8 @@ fn sync_custom_environment_path() -> Result<()> {
     ----- stdout -----
 
     ----- stderr -----
+    Using Python 3.12.[X] interpreter at: [PYTHON-3.12]
+    Creating virtualenv at: .venv
     Resolved 2 packages in [TIME]
     Prepared 1 package in [TIME]
     Installed 1 package in [TIME]
@@ -1733,6 +1735,52 @@ fn sync_custom_environment_path() -> Result<()> {
         .child(".venv")
         .assert(predicate::path::is_dir());
 
+    // If the directory already exists and is not a virtual environment we should fail with an error
+    fs_err::remove_dir_all(context.temp_dir.join("foo"))?;
+    fs_err::create_dir(context.temp_dir.join("foo"))?;
+    fs_err::write(context.temp_dir.join("foo").join("file"), b"")?;
+    uv_snapshot!(context.filters(), context.sync().env("UV_PROJECT_ENVIRONMENT", "foo"), @r###"
+    success: false
+    exit_code: 2
+    ----- stdout -----
+
+    ----- stderr -----
+    warning: Ignoring existing virtual environment linked to non-existent Python interpreter: foo/bin/python3
+    Using Python 3.12.[X] interpreter at: [PYTHON-3.12]
+    error: Project virtual environment directory `[TEMP_DIR]/foo` cannot be used because it has existing, non-virtual environment content
+    "###);
+
+    // But if it's just an incompatible virtual environment...
+    fs_err::remove_dir_all(context.temp_dir.join("foo"))?;
+    uv_snapshot!(context.filters(), context.venv().arg("foo").arg("--python").arg("3.11"), @r###"
+    success: true
+    exit_code: 0
+    ----- stdout -----
+
+    ----- stderr -----
+    Using Python 3.11.[X] interpreter at: [PYTHON-3.11]
+    Creating virtualenv at: foo
+    Activate with: source foo/bin/activate
+    "###);
+
+    // Even with some extraneous content...
+    fs_err::write(context.temp_dir.join("foo").join("file"), b"")?;
+
+    // We can delete and use it
+    uv_snapshot!(context.filters(), context.sync().env("UV_PROJECT_ENVIRONMENT", "foo"), @r###"
+    success: true
+    exit_code: 0
+    ----- stdout -----
+
+    ----- stderr -----
+    Using Python 3.12.[X] interpreter at: [PYTHON-3.12]
+    Removed virtual environment at: foo
+    Creating virtualenv at: foo
+    Resolved 2 packages in [TIME]
+    Installed 1 package in [TIME]
+     + iniconfig==2.0.0
+    "###);
+
     Ok(())
 }