diff --git a/scripts/functional_tests.py b/scripts/functional_tests.py
index 1cdeb014bac..67fb063293e 100644
--- a/scripts/functional_tests.py
+++ b/scripts/functional_tests.py
@@ -28,21 +28,17 @@ def main():
     testing_installed_tools = _check_arg( '-installed' )
     datatypes_conf_override = None
 
+    default_tool_conf = None
     testing_shed_tools = testing_migrated_tools or testing_installed_tools
-    if testing_shed_tools:
-        # We need the upload tool for functional tests, so we'll create a temporary tool panel config that defines it.
-        tool_config_file = driver_util.FRAMEWORK_UPLOAD_TOOL_CONF
-    else:
+    if not testing_shed_tools:
         framework_test = _check_arg( '-framework' )  # Run through suite of tests testing framework.
         if framework_test:
-            tool_conf = driver_util.FRAMEWORK_SAMPLE_TOOLS_CONF
+            default_tool_conf = driver_util.FRAMEWORK_SAMPLE_TOOLS_CONF
             datatypes_conf_override = driver_util.FRAMEWORK_DATATYPES_CONF
         else:
             # Use tool_conf.xml toolbox.
-            tool_conf = None
             if _check_arg( '-with_framework_test_tools' ):
-                tool_conf = "%s,%s" % ( 'config/tool_conf.xml.sample', driver_util.FRAMEWORK_SAMPLE_TOOLS_CONF )
-        tool_config_file = os.environ.get( 'GALAXY_TEST_TOOL_CONF', tool_conf )
+                default_tool_conf = "%s,%s" % ( 'config/tool_conf.xml.sample', driver_util.FRAMEWORK_SAMPLE_TOOLS_CONF )
 
     start_server = 'GALAXY_TEST_EXTERNAL' not in os.environ
 
@@ -57,6 +53,7 @@ def main():
             galaxy_db_path,
             use_test_file_dir=not testing_shed_tools,
             default_install_db_merged=True,
+            default_tool_conf=default_tool_conf,
         )
 
     app = None
@@ -65,7 +62,6 @@ def main():
     if start_server:
         # ---- Build Application --------------------------------------------------
         kwargs = dict( shed_tool_data_table_config=shed_tool_data_table_config,
-                       tool_config_file=tool_config_file,
                        update_integrated_tool_panel=False, )
         kwargs.update(galaxy_config)
         if datatypes_conf_override:
diff --git a/test/base/driver_util.py b/test/base/driver_util.py
index 7453633056b..f48b5344b6d 100644
--- a/test/base/driver_util.py
+++ b/test/base/driver_util.py
@@ -96,6 +96,8 @@ def setup_galaxy_config(
     default_install_db_merged=True,
     default_tool_data_table_config_path=None,
     enable_tool_shed_check=False,
+    default_tool_conf=None,
+    shed_tool_conf=None,
 ):
     """Setup environment and build config for test Galaxy instance."""
     if not os.path.exists(tmpdir):
@@ -136,6 +138,14 @@ def setup_galaxy_config(
     # For storing Data Manager outputs and .loc files so that real ones don't get clobbered
     galaxy_data_manager_data_path = tempfile.mkdtemp(prefix='data_manager_tool-data', dir=tmpdir)
 
+    tool_conf = os.environ.get('GALAXY_TEST_TOOL_CONF', default_tool_conf)
+    if tool_conf is None:
+        # As a fallback always at least allow upload.
+        tool_conf = FRAMEWORK_UPLOAD_TOOL_CONF
+
+    if shed_tool_conf is not None:
+        tool_conf = "%s,%s" % (tool_conf, shed_tool_conf)
+
     config = dict(
         admin_users='test@bx.psu.edu',
         allow_library_path_paste=True,
@@ -159,6 +169,7 @@ def setup_galaxy_config(
         running_functional_tests=True,
         template_cache_path=template_cache_path,
         template_path='templates',
+        tool_config_file=tool_conf,
         tool_data_table_config_path=tool_data_table_config_path,
         tool_parse_help=False,
         tool_path=tool_path,
diff --git a/test/tool_shed/functional_tests.py b/test/tool_shed/functional_tests.py
index ce04f3ea45a..97f591c9263 100644
--- a/test/tool_shed/functional_tests.py
+++ b/test/tool_shed/functional_tests.py
@@ -57,7 +57,6 @@ def main():
     shed_tool_data_table_conf_file = os.environ.get( 'TOOL_SHED_TEST_TOOL_DATA_TABLE_CONF', os.path.join( tool_shed_test_tmp_dir, 'shed_tool_data_table_conf.xml' ) )
     galaxy_shed_data_manager_conf_file = os.environ.get( 'GALAXY_SHED_DATA_MANAGER_CONF', os.path.join( tool_shed_test_tmp_dir, 'test_shed_data_manager_conf.xml' ) )
     default_tool_data_table_config_path = os.path.join( tool_shed_test_tmp_dir, 'tool_data_table_conf.xml' )
-    galaxy_tool_conf_file = os.environ.get( 'GALAXY_TEST_TOOL_CONF', driver_util.FRAMEWORK_UPLOAD_TOOL_CONF )
     galaxy_shed_tool_conf_file = os.environ.get( 'GALAXY_TEST_SHED_TOOL_CONF', os.path.join( tool_shed_test_tmp_dir, 'test_shed_tool_conf.xml' ) )
     galaxy_migrated_tool_conf_file = os.environ.get( 'GALAXY_TEST_MIGRATED_TOOL_CONF', os.path.join( tool_shed_test_tmp_dir, 'test_migrated_tool_conf.xml' ) )
     galaxy_tool_sheds_conf_file = os.environ.get( 'GALAXY_TEST_TOOL_SHEDS_CONF', os.path.join( tool_shed_test_tmp_dir, 'test_sheds_conf.xml' ) )
@@ -137,7 +136,7 @@ def main():
                        shed_tool_data_table_config=shed_tool_data_table_conf_file,
                        shed_tool_path=galaxy_shed_tool_path,
                        tool_data_path=tool_data_path,
-                       tool_config_file=[ galaxy_tool_conf_file, galaxy_shed_tool_conf_file ],
+
                        tool_sheds_config_file=galaxy_tool_sheds_conf_file )
         kwargs.update(
             driver_util.setup_galaxy_config(
@@ -146,6 +145,7 @@ def main():
                 default_install_db_merged=False,
                 default_tool_data_table_config_path=default_tool_data_table_config_path,
                 enable_tool_shed_check=True,
+                shed_tool_conf=galaxy_shed_tool_conf_file,
             )
         )
         print "Galaxy database connection:", kwargs["database_connection"]