diff --git a/crates/uv/src/commands/project/mod.rs b/crates/uv/src/commands/project/mod.rs
index 1a0274cac..2b1af8ebc 100644
--- a/crates/uv/src/commands/project/mod.rs
+++ b/crates/uv/src/commands/project/mod.rs
@@ -920,7 +920,9 @@ impl ProjectInterpreter {
                         ));
                     }
                     InvalidEnvironmentKind::MissingExecutable(_) => {
-                        if fs_err::read_dir(&root).is_ok_and(|mut dir| dir.next().is_some()) {
+                        if fs_err::read_dir(&root).is_ok_and(|mut dir| dir.next().is_some())
+                            && !root.join(".uv-partial-rm").try_exists().unwrap_or(false)
+                        {
                             return Err(ProjectError::InvalidProjectEnvironmentDir(
                                 root,
                                 "it is not a valid Python environment (no Python executable was found)"
@@ -1294,6 +1296,9 @@ impl ProjectEnvironment {
                         // Unless it's empty, in which case we just ignore it
                         if root.read_dir().is_ok_and(|mut dir| dir.next().is_none()) {
                             false
+                        // Or, if there's a marker file indicating a previous removal failed
+                        } else if root.join(".uv-partial-rm").try_exists().unwrap_or(false) {
+                            true
                         } else {
                             return Err(ProjectError::InvalidProjectEnvironmentDir(
                                 root,
@@ -1363,7 +1368,23 @@ impl ProjectEnvironment {
                             )?;
                         }
                         Err(e) if e.kind() == std::io::ErrorKind::NotFound => {}
-                        Err(e) => return Err(e.into()),
+                        Err(e) => {
+                            // Try to write a marker to indicate that we failed to remove the entire
+                            // environment, so when the next command runs we can attempt to remove
+                            // it even if a `pyvenv.cfg` marker was removed
+                            match fs_err::write(root.join(".uv-partial-rm"), "") {
+                                Ok(()) => {
+                                    debug!(
+                                        "Wrote `.uv-partial-rm` marker to partially deleted environment: {}",
+                                        root.user_display().cyan()
+                                    );
+                                }
+                                Err(err) => {
+                                    debug!("Failed to write `.uv-partial-rm` marker: {err}");
+                                }
+                            }
+                            return Err(e.into());
+                        }
                     }
                 }
 
diff --git a/crates/uv/tests/it/sync.rs b/crates/uv/tests/it/sync.rs
index d4479296a..d6cc7f26a 100644
--- a/crates/uv/tests/it/sync.rs
+++ b/crates/uv/tests/it/sync.rs
@@ -5000,6 +5000,59 @@ fn sync_update_project() -> Result<()> {
     Ok(())
 }
 
+#[test]
+fn sync_no_pyvenv_cfg() -> Result<()> {
+    let context = TestContext::new("3.12");
+
+    let pyproject_toml = context.temp_dir.child("pyproject.toml");
+    pyproject_toml.write_str(
+        r#"
+        [project]
+        name = "my-project"
+        version = "0.1.0"
+        requires-python = ">=3.12"
+        dependencies = ["iniconfig"]
+        "#,
+    )?;
+
+    // Break the virtual environment
+    fs_err::remove_dir_all(
+        context
+            .venv
+            .join(if cfg!(windows) { "Scripts" } else { "bin" }),
+    )?;
+    fs_err::remove_file(context.venv.join("pyvenv.cfg"))?;
+
+    // Running `uv sync` won't create the venv
+    uv_snapshot!(context.filters(), context.sync(), @r"
+    success: false
+    exit_code: 2
+    ----- stdout -----
+
+    ----- stderr -----
+    error: Project virtual environment directory `[VENV]/` cannot be used because it is not a valid Python environment (no Python executable was found)
+    ");
+
+    // Write the marker that indicates the environment was partially removed by uv
+    fs_err::write(context.venv.join(".uv-partial-rm"), "")?;
+    uv_snapshot!(context.filters(), context.sync(), @r"
+    success: true
+    exit_code: 0
+    ----- stdout -----
+
+    ----- stderr -----
+    Using CPython 3.12.[X] interpreter at: [PYTHON-3.12]
+    Removed virtual environment at: .venv
+    Creating virtual environment at: .venv
+    Resolved 2 packages in [TIME]
+    Prepared 1 package in [TIME]
+    Installed 1 package in [TIME]
+     + iniconfig==2.0.0
+    ");
+
+    Ok(())
+}
+
 #[test]
 fn sync_environment_prompt() -> Result<()> {
     let context = TestContext::new_with_versions(&["3.12"]);