diff --git a/renku/api/storage.py b/renku/api/storage.py
index 83de34bc12..5db59a83ca 100644
--- a/renku/api/storage.py
+++ b/renku/api/storage.py
@@ -31,6 +31,10 @@
 
 HAS_LFS = call(['git', 'lfs'], stdout=PIPE, stderr=STDOUT) == 0
 
+# Batch size for when renku is expanding a large list
+# of files into an argument string.
+ARGUMENT_BATCH_SIZE = 100
+
 
 @attr.s
 class StorageApiMixin(RepositoryApiMixin):
@@ -105,6 +109,7 @@ def untrack_paths_from_storage(self, *paths):
 
     def pull_paths_from_storage(self, *paths):
         """Pull paths from LFS."""
+        import math
         if self.use_external_storage and self.external_storage_installed:
             client_dict = defaultdict(list)
 
@@ -115,12 +120,22 @@ def pull_paths_from_storage(self, *paths):
                 client_dict[client.path].append(str(path))
 
             for client_path, paths in client_dict.items():
-                run(
-                    self._CMD_STORAGE_PULL + [shlex.quote(','.join(paths))],
-                    cwd=str(client_path.absolute()),
-                    stdout=PIPE,
-                    stderr=STDOUT,
-                )
+                for ibatch in range(
+                    math.ceil(len(paths) / ARGUMENT_BATCH_SIZE)
+                ):
+                    run(
+                        self._CMD_STORAGE_PULL + [
+                            shlex.quote(
+                                ','.join(
+                                    paths[ibatch * ARGUMENT_BATCH_SIZE:
+                                          (ibatch + 1) * ARGUMENT_BATCH_SIZE]
+                                )
+                            )
+                        ],
+                        cwd=str(client_path.absolute()),
+                        stdout=PIPE,
+                        stderr=STDOUT,
+                    )
         elif self.use_external_storage:
             raise errors.ExternalStorageNotInstalled(self.repo)
 
diff --git a/tests/test_cli.py b/tests/test_cli.py
index 635af28704..a8f7d7a49a 100644
--- a/tests/test_cli.py
+++ b/tests/test_cli.py
@@ -103,6 +103,20 @@ def test_run_simple(runner, project):
     assert '.renku/workflow/' in result.output
 
 
+def test_run_many_args(client, run):
+    """Test a renku run command which implicitly relies on many inputs."""
+
+    os.mkdir('files')
+    output = 'output.txt'
+    for i in range(5003):
+        os.system('touch files/{}.txt'.format(i))
+    client.repo.index.add(['files/'])
+    client.repo.index.commit('add many files')
+
+    exit_code = run(args=('run', 'ls', 'files/'), stdout=output)
+    assert 0 == exit_code
+
+
 _CMD_EXIT_2 = ['bash', '-c', 'exit 2']