diff --git a/src/scancode/cli.py b/src/scancode/cli.py
index 1376c6cfee..faa3375c5c 100644
--- a/src/scancode/cli.py
+++ b/src/scancode/cli.py
@@ -1070,6 +1070,27 @@ def echo_func(*_args, **_kwargs):
             results = get_results(codebase, as_list=True, **requested_options)
         elif return_codebase:
             results = codebase
+            # Strip root from paths when strip_root is enabled.
+            # See https://github.com/aboutcode-org/scancode-toolkit/issues/2985
+            if strip_root and not codebase.has_single_resource:
+                from commoncode.resource import strip_first_path_segment
+                new_resources_by_path = {}
+                for old_path, resource in list(codebase.resources_by_path.items()):
+                    stripped_path = strip_first_path_segment(old_path)
+                    resource.path = stripped_path
+                    new_resources_by_path[stripped_path] = resource
+                codebase.resources_by_path = new_resources_by_path
+                
+                # Fix parent() to handle empty parent_path for direct children of root.
+                # commoncode's parent() uses `return path and get_resource(path)` which 
+                # returns '' (empty string) when path is '', breaking tree traversal.
+                original_parent = codebase.resource_class.parent
+                def patched_parent(self, codebase_arg):
+                    parent_path = self.parent_path()
+                    if parent_path == '':
+                        return codebase_arg.root
+                    return original_parent(self, codebase_arg)
+                codebase.resource_class.parent = patched_parent
 
     finally:
         # remove temporary files