diff --git a/crates/uv-virtualenv/src/lib.rs b/crates/uv-virtualenv/src/lib.rs
index b04a500a5..bcf1e9f97 100644
--- a/crates/uv-virtualenv/src/lib.rs
+++ b/crates/uv-virtualenv/src/lib.rs
@@ -6,7 +6,7 @@ use thiserror::Error;
 use uv_configuration::PreviewMode;
 use uv_python::{Interpreter, PythonEnvironment};
 
-pub use virtualenv::OnExisting;
+pub use virtualenv::{OnExisting, remove_virtualenv};
 
 mod virtualenv;
 
diff --git a/crates/uv-virtualenv/src/virtualenv.rs b/crates/uv-virtualenv/src/virtualenv.rs
index fb22a0724..2227b71b9 100644
--- a/crates/uv-virtualenv/src/virtualenv.rs
+++ b/crates/uv-virtualenv/src/virtualenv.rs
@@ -97,7 +97,8 @@ pub(crate) fn create(
                 }
                 OnExisting::Remove => {
                     debug!("Removing existing {name} due to `--clear`");
-                    remove_venv_directory(location)?;
+                    remove_virtualenv(location)?;
+                    fs::create_dir_all(location)?;
                 }
                 OnExisting::Fail
                     if location
@@ -110,7 +111,8 @@ pub(crate) fn create(
                     match confirm_clear(location, name)? {
                         Some(true) => {
                             debug!("Removing existing {name} due to confirmation");
-                            remove_venv_directory(location)?;
+                            remove_virtualenv(location)?;
+                            fs::create_dir_all(location)?;
                         }
                         Some(false) => {
                             let hint = format!(
@@ -566,9 +568,10 @@ fn confirm_clear(location: &Path, name: &'static str) -> Result<Option<bool>, io
     }
 }
 
-fn remove_venv_directory(location: &Path) -> Result<(), Error> {
-    // On Windows, if the current executable is in the directory, guard against
-    // self-deletion.
+/// Perform a safe removal of a virtual environment.
+pub fn remove_virtualenv(location: &Path) -> Result<(), Error> {
+    // On Windows, if the current executable is in the directory, defer self-deletion since Windows
+    // won't let you unlink a running executable.
     #[cfg(windows)]
     if let Ok(itself) = std::env::current_exe() {
         let target = std::path::absolute(location)?;
@@ -578,8 +581,27 @@ fn remove_venv_directory(location: &Path) -> Result<(), Error> {
         }
     }
 
+    // We defer removal of the `pyvenv.cfg` until the end, so if we fail to remove the environment,
+    // uv can still identify it as a Python virtual environment that can be deleted.
+    for entry in fs::read_dir(location)? {
+        let entry = entry?;
+        let path = entry.path();
+        if path == location.join("pyvenv.cfg") {
+            continue;
+        }
+        if path.is_dir() {
+            fs::remove_dir_all(&path)?;
+        } else {
+            fs::remove_file(&path)?;
+        }
+    }
+
+    match fs::remove_file(location.join("pyvenv.cfg")) {
+        Ok(()) => {}
+        Err(err) if err.kind() == io::ErrorKind::NotFound => {}
+        Err(err) => return Err(err.into()),
+    }
     fs::remove_dir_all(location)?;
-    fs::create_dir_all(location)?;
 
     Ok(())
 }
diff --git a/crates/uv/src/commands/project/mod.rs b/crates/uv/src/commands/project/mod.rs
index becd2a26e..3ad530edd 100644
--- a/crates/uv/src/commands/project/mod.rs
+++ b/crates/uv/src/commands/project/mod.rs
@@ -43,6 +43,7 @@ use uv_scripts::Pep723ItemRef;
 use uv_settings::PythonInstallMirrors;
 use uv_static::EnvVars;
 use uv_types::{BuildIsolation, EmptyInstalledPackages, HashStrategy};
+use uv_virtualenv::remove_virtualenv;
 use uv_warnings::{warn_user, warn_user_once};
 use uv_workspace::dependency_groups::DependencyGroupError;
 use uv_workspace::pyproject::PyProjectToml;
@@ -1373,7 +1374,7 @@ impl ProjectEnvironment {
 
                 // Remove the existing virtual environment if it doesn't meet the requirements.
                 if replace {
-                    match fs_err::remove_dir_all(&root) {
+                    match remove_virtualenv(&root) {
                         Ok(()) => {
                             writeln!(
                                 printer.stderr(),
@@ -1381,8 +1382,9 @@ impl ProjectEnvironment {
                                 root.user_display().cyan()
                             )?;
                         }
-                        Err(e) if e.kind() == std::io::ErrorKind::NotFound => {}
-                        Err(e) => return Err(e.into()),
+                        Err(uv_virtualenv::Error::Io(err))
+                            if err.kind() == std::io::ErrorKind::NotFound => {}
+                        Err(err) => return Err(err.into()),
                     }
                 }