diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index 922c6f42357..f1ba0711c10 100755
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -255,6 +255,19 @@ class ToolBox(BaseGalaxyToolBox):
             app=app,
         )
 
+    def can_load_config_file(self, config_filename):
+        if config_filename == self.app.config.shed_tool_config_file and not self.app.config.shed_tool_config_file_set:
+            if self.dynamic_confs():
+                # Do not load or create a default shed_tool_config_file if another shed_tool_config file has already been loaded
+                return False
+        elif self.app.config.tool_config_file_set:
+            log.warning(
+                "The default shed tool config file (%s) has been added to the tool_config_file option, if this is "
+                "not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool "
+                "config file", self.app.config.shed_tool_config_file
+            )
+        return True
+
     def has_reloaded(self, other_toolbox):
         return self._reload_count != other_toolbox._reload_count
 
diff --git a/lib/galaxy/tools/toolbox/base.py b/lib/galaxy/tools/toolbox/base.py
index 536cc6f876a..1df15984b40 100644
--- a/lib/galaxy/tools/toolbox/base.py
+++ b/lib/galaxy/tools/toolbox/base.py
@@ -127,6 +127,9 @@ class AbstractToolBox(Dictifiable, ManagesIntegratedToolPanelMixin):
     def create_dynamic_tool(self, dynamic_tool):
         raise NotImplementedError()
 
+    def can_load_config_file(self, config_filename):
+        return True
+
     def _init_tools_from_configs(self, config_filenames):
         """ Read through all tool config files and initialize tools in each
         with init_tools_from_config below.
@@ -141,16 +144,8 @@ class AbstractToolBox(Dictifiable, ManagesIntegratedToolPanelMixin):
                 config_filenames.remove(config_filename)
                 config_filenames.extend(directory_config_files)
         for config_filename in config_filenames:
-            if config_filename == self.app.config.shed_tool_config_file and not self.app.config.shed_tool_config_file_set:
-                if self.dynamic_confs():
-                    # Do not load or create a default shed_tool_config_file if another shed_tool_config file has already been loaded
-                    continue
-                elif self.app.config.tool_config_file_set:
-                    log.warning(
-                        "The default shed tool config file (%s) has been added to the tool_config_file option, if this is "
-                        "not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool "
-                        "config file", self.app.config.shed_tool_config_file
-                    )
+            if not self.can_load_config_file(config_filename):
+                continue
             try:
                 self._init_tools_from_config(config_filename)
             except ParseError:
diff --git a/test/unit/unittest_utils/galaxy_mock.py b/test/unit/unittest_utils/galaxy_mock.py
index f86abd25987..38f0d8cd367 100644
--- a/test/unit/unittest_utils/galaxy_mock.py
+++ b/test/unit/unittest_utils/galaxy_mock.py
@@ -145,6 +145,8 @@ class MockAppConfig(Bunch):
         self.builds_file_path = os.path.join('tool-data', 'shared', 'ucsc', 'builds.txt.sample')
 
         self.migrated_tools_config = "/tmp/migrated_tools_conf.xml"
+        self.shed_tool_config_file = "config/shed_tool_conf.xml"
+        self.shed_tool_config_file_set = False
         self.preserve_python_environment = "always"
         self.enable_beta_gdpr = False
         self.legacy_eager_objectstore_initialization = True