diff --git a/crates/mapdiffbot2/src/git_operations.rs b/crates/mapdiffbot2/src/git_operations.rs
index 7b4e9eb9..b46ad884 100644
--- a/crates/mapdiffbot2/src/git_operations.rs
+++ b/crates/mapdiffbot2/src/git_operations.rs
@@ -1,7 +1,7 @@
 use eyre::{Context, Result};
 use std::path::Path;
 
-use git2::{build::CheckoutBuilder, FetchOptions, Repository, SubmoduleUpdateOptions};
+use git2::{build::CheckoutBuilder, FetchOptions, Repository};
 
 pub fn fetch_and_get_branches<'a>(
     base_sha: &str,
@@ -178,23 +178,6 @@ pub fn with_checkout<T>(
 ) -> Result<T> {
     repo.set_head(checkout_ref.name().unwrap())?;
     repo.checkout_head(Some(CheckoutBuilder::new().force().remove_untracked(true)))?;
-
-    if let Ok(submodules) = repo.submodules() {
-        submodules.into_iter().for_each(|mut submodule| {
-            _ = submodule.update(
-                true,
-                Some(
-                    SubmoduleUpdateOptions::default()
-                        .allow_fetch(true)
-                        .checkout({
-                            let mut builder = CheckoutBuilder::new();
-                            builder.force().remove_untracked(true);
-                            builder
-                        }),
-                ),
-            );
-        })
-    }
     commit_all_stragglers(repo)?;
     f()
 }
@@ -206,23 +189,6 @@ pub fn checkout_to(checkout_ref: &str, repo: &Repository) -> Result<()> {
             .unwrap(),
     )?;
     repo.checkout_head(Some(CheckoutBuilder::new().force().remove_untracked(true)))?;
-
-    if let Ok(submodules) = repo.submodules() {
-        submodules.into_iter().for_each(|mut submodule| {
-            _ = submodule.update(
-                true,
-                Some(
-                    SubmoduleUpdateOptions::default()
-                        .allow_fetch(true)
-                        .checkout({
-                            let mut builder = CheckoutBuilder::new();
-                            builder.force().remove_untracked(true);
-                            builder
-                        }),
-                ),
-            );
-        })
-    }
     commit_all_stragglers(repo)?;
     Ok(())
 }
diff --git a/crates/mapdiffbot2/src/job_processor.rs b/crates/mapdiffbot2/src/job_processor.rs
index 725fc7ac..9f5b1fb9 100644
--- a/crates/mapdiffbot2/src/job_processor.rs
+++ b/crates/mapdiffbot2/src/job_processor.rs
@@ -416,7 +416,19 @@ pub fn do_job(job: Job, blob_client: Azure) -> Result<CheckOutputs> {
     let modified_files = filter_on_status(ChangeType::Modified);
     let removed_files = filter_on_status(ChangeType::Deleted);
 
-    let repository = git2::Repository::open(&repo_dir).wrap_err("Opening repository")?;
+    let mut repository = git2::Repository::open(&repo_dir).wrap_err("Opening repository")?;
+
+    //has to be done this way because of borrowing rules
+    if let Ok(submod_names) = repository.submodules().map(|submodules| {
+        submodules
+            .into_iter()
+            .filter_map(|submod| submod.name().map(|refstr| refstr.to_owned()))
+            .collect::<Vec<_>>()
+    }) {
+        submod_names.into_iter().for_each(|name| {
+            _ = repository.submodule_set_ignore(&name, git2::SubmoduleIgnore::All);
+        });
+    };
 
     if !clone_required {
         repository.remote_set_url("origin", &url)?;