diff --git a/crates/uv/src/commands/project/init.rs b/crates/uv/src/commands/project/init.rs
index 98845d1f4..ccf5d9118 100644
--- a/crates/uv/src/commands/project/init.rs
+++ b/crates/uv/src/commands/project/init.rs
@@ -769,6 +769,10 @@ impl InitProjectKind {
     ) -> Result<()> {
         fs_err::create_dir_all(path)?;
 
+        // Initialize the version control system first so that Git configuration can properly
+        // read conditional includes that depend on the repository path.
+        init_vcs(path, vcs)?;
+
         // Do no fill in `authors` for non-packaged applications unless explicitly requested.
         let author_from = author_from.unwrap_or_else(|| {
             if package {
@@ -828,9 +832,6 @@ impl InitProjectKind {
         }
         fs_err::write(path.join("pyproject.toml"), pyproject)?;
 
-        // Initialize the version control system.
-        init_vcs(path, vcs)?;
-
         Ok(())
     }
 
@@ -855,6 +856,10 @@ impl InitProjectKind {
 
         fs_err::create_dir_all(path)?;
 
+        // Initialize the version control system first so that Git configuration can properly
+        // read conditional includes that depend on the repository path.
+        init_vcs(path, vcs)?;
+
         let author = get_author_info(path, author_from.unwrap_or_default());
 
         // Create the `pyproject.toml`
@@ -880,9 +885,6 @@ impl InitProjectKind {
             generate_package_scripts(name, path, build_backend, true)?;
         }
 
-        // Initialize the version control system.
-        init_vcs(path, vcs)?;
-
         Ok(())
     }
 }