diff --git a/src/main.rs b/src/main.rs
index 0e7d2545..3c2551a5 100644
--- a/src/main.rs
+++ b/src/main.rs
@@ -172,37 +172,37 @@ fn run() -> Result<()> {
         if config.should_run(Step::Emacs) {
             if !emacs.is_doom() {
                 if let Some(directory) = emacs.directory() {
-                    git_repos.insert(directory);
+                    git_repos.insert_if_repo(directory);
                 }
             }
-            git_repos.insert(base_dirs.home_dir().join(".doom.d"));
+            git_repos.insert_if_repo(base_dirs.home_dir().join(".doom.d"));
         }
 
         if config.should_run(Step::Vim) {
-            git_repos.insert(base_dirs.home_dir().join(".vim"));
-            git_repos.insert(base_dirs.home_dir().join(".config/nvim"));
+            git_repos.insert_if_repo(base_dirs.home_dir().join(".vim"));
+            git_repos.insert_if_repo(base_dirs.home_dir().join(".config/nvim"));
         }
 
         #[cfg(unix)]
         {
-            git_repos.insert(zsh::zshrc(&base_dirs));
-            git_repos.insert(base_dirs.home_dir().join(".tmux"));
-            git_repos.insert(base_dirs.home_dir().join(".config/fish"));
-            git_repos.insert(base_dirs.config_dir().join("openbox"));
-            git_repos.insert(base_dirs.config_dir().join("bspwm"));
-            git_repos.insert(base_dirs.config_dir().join("i3"));
-            git_repos.insert(base_dirs.config_dir().join("sway"));
+            git_repos.insert_if_repo(zsh::zshrc(&base_dirs));
+            git_repos.insert_if_repo(base_dirs.home_dir().join(".tmux"));
+            git_repos.insert_if_repo(base_dirs.home_dir().join(".config/fish"));
+            git_repos.insert_if_repo(base_dirs.config_dir().join("openbox"));
+            git_repos.insert_if_repo(base_dirs.config_dir().join("bspwm"));
+            git_repos.insert_if_repo(base_dirs.config_dir().join("i3"));
+            git_repos.insert_if_repo(base_dirs.config_dir().join("sway"));
         }
 
         #[cfg(windows)]
-        git_repos.insert(
+        git_repos.insert_if_repo(
             base_dirs
                 .data_local_dir()
                 .join("Packages/Microsoft.WindowsTerminal_8wekyb3d8bbwe/LocalState"),
         );
 
         if let Some(profile) = powershell.profile() {
-            git_repos.insert(profile);
+            git_repos.insert_if_repo(profile);
         }
     }
 
diff --git a/src/steps/git.rs b/src/steps/git.rs
index 58209b78..aae490e6 100644
--- a/src/steps/git.rs
+++ b/src/steps/git.rs
@@ -1,7 +1,7 @@
 use crate::error::{SkipStep, TopgradeError};
 use crate::executor::{CommandExt, RunType};
 use crate::terminal::print_separator;
-use crate::utils::which;
+use crate::utils::{which, PathExt};
 use anyhow::Result;
 use console::style;
 use glob::{glob_with, MatchOptions};
@@ -221,17 +221,35 @@ impl<'a> Repositories<'a> {
         }
     }
 
-    pub fn insert<P: AsRef<Path>>(&mut self, path: P) {
+    pub fn insert_if_repo<P: AsRef<Path>>(&mut self, path: P) -> bool {
         if let Some(repo) = self.git.get_repo_root(path) {
             self.repositories.insert(repo);
+            true
+        } else {
+            false
         }
     }
 
     pub fn glob_insert(&mut self, pattern: &str) {
         if let Ok(glob) = glob_with(pattern, self.glob_match_options) {
+            let mut last_git_repo: Option<PathBuf> = None;
             for entry in glob {
                 match entry {
-                    Ok(path) => self.insert(path),
+                    Ok(path) => {
+                        if let Some(last_git_repo) = &last_git_repo {
+                            if path.is_descendant_of(&last_git_repo) {
+                                debug!(
+                                    "Skipping {} because it's a decendant of last known repo {}",
+                                    path.display(),
+                                    last_git_repo.display()
+                                );
+                                continue;
+                            }
+                        }
+                        if self.insert_if_repo(&path) {
+                            last_git_repo = Some(path);
+                        }
+                    }
                     Err(e) => {
                         error!("Error in path {}", e);
                     }