diff --git a/project.py b/project.py
index 37cec98f..53350b7f 100644
--- a/project.py
+++ b/project.py
@@ -642,6 +642,10 @@ class Project:
         # project containing repo hooks.
         self.enabled_repo_hooks = []
 
+        # This will be updated later if the project has submodules and
+        # if they will be synced.
+        self.has_subprojects = False
+
     def RelPath(self, local=True):
         """Return the path for the project relative to a manifest.
 
@@ -1560,6 +1564,11 @@ class Project:
             return
 
         self._InitWorkTree(force_sync=force_sync, submodules=submodules)
+        # TODO(https://git-scm.com/docs/git-worktree#_bugs): Re-evaluate if
+        # submodules can be init when using worktrees once its support is
+        # complete.
+        if self.has_subprojects and not self.use_git_worktrees:
+            self._InitSubmodules()
         all_refs = self.bare_ref.all
         self.CleanPublishedCache(all_refs)
         revid = self.GetRevisionId(all_refs)
@@ -2347,6 +2356,8 @@ class Project:
             )
             result.append(subproject)
             result.extend(subproject.GetDerivedSubprojects())
+        if result:
+            self.has_subprojects = True
         return result
 
     def EnableRepositoryExtension(self, key, value="true", version=1):
@@ -2997,6 +3008,17 @@ class Project:
                 project=self.name,
             )
 
+    def _InitSubmodules(self, quiet=True):
+        """Initialize the submodules for the project."""
+        cmd = ["submodule", "init"]
+        if quiet:
+            cmd.append("-q")
+        if GitCommand(self, cmd).Wait() != 0:
+            raise GitError(
+                f"{self.name} submodule init",
+                project=self.name,
+            )
+
     def _Rebase(self, upstream, onto=None):
         cmd = ["rebase"]
         if onto is not None: