diff --git a/git-branchless-lib/src/core/config.rs b/git-branchless-lib/src/core/config.rs
index 248525a36..82eac41b1 100644
--- a/git-branchless-lib/src/core/config.rs
+++ b/git-branchless-lib/src/core/config.rs
@@ -54,7 +54,13 @@ pub fn get_main_worktree_hooks_dir(
     let hooks_path = if result.exit_code.is_success() {
         let path = String::from_utf8(result.stdout)
             .context("Decoding git config output for hooks path")?;
-        PathBuf::from(path.strip_suffix('\n').unwrap_or(&path))
+
+        let path = PathBuf::from(path.strip_suffix('\n').unwrap_or(&path));
+
+        repo.get_working_copy_path()
+            .as_deref()
+            .unwrap_or_else(|| repo.get_path())
+            .join(path)
     } else {
         get_default_hooks_dir(repo)?
     };
diff --git a/git-branchless/tests/test_init.rs b/git-branchless/tests/test_init.rs
index 82be1b2d1..d5a4ce8b2 100644
--- a/git-branchless/tests/test_init.rs
+++ b/git-branchless/tests/test_init.rs
@@ -547,7 +547,7 @@ fn test_init_core_hooks_path_warning() -> eyre::Result<()> {
         Auto-detected your main branch as: master
         If this is incorrect, run: git branchless init --main-branch <branch>
         Installing hooks: post-applypatch, post-checkout, post-commit, post-merge, post-rewrite, pre-auto-gc, reference-transaction
-        Warning: the configuration value core.hooksPath was set to: my-hooks,
+        Warning: the configuration value core.hooksPath was set to: <repo-path>/my-hooks,
         which is not the expected default value of: <repo-path>/.git/hooks
         The Git hooks above may have been installed to an unexpected global location.
         Successfully installed git-branchless.
@@ -600,7 +600,7 @@ hooksPath = my-hooks
         Auto-detected your main branch as: master
         If this is incorrect, run: git branchless init --main-branch <branch>
         Installing hooks: post-applypatch, post-checkout, post-commit, post-merge, post-rewrite, pre-auto-gc, reference-transaction
-        Warning: the configuration value core.hooksPath was set to: my-hooks,
+        Warning: the configuration value core.hooksPath was set to: <repo-path>/my-hooks,
         which is not the expected default value of: <repo-path>/.git/hooks
         The Git hooks above may have been installed to an unexpected global location.
         Successfully installed git-branchless.