diff --git a/lib/galaxy/jobs/__init__.py b/lib/galaxy/jobs/__init__.py
index 137e81f0b6b..878421d0ac9 100644
--- a/lib/galaxy/jobs/__init__.py
+++ b/lib/galaxy/jobs/__init__.py
@@ -1665,7 +1665,7 @@ class JobWrapper( object ):
             if metadata_tool is not None:
                 # Due to tool shed hacks for migrate and installed tool tests...
                 # see (``setup_shed_tools_for_test`` in test/base/driver_util.py).
-                dependency_shell_commands = metadata_tool.build_dependency_shell_commands(job_directory=self.working_directory)
+                dependency_shell_commands = metadata_tool.build_dependency_shell_commands(job_directory=self.working_directory, metadata=True)
                 if dependency_shell_commands:
                     dependency_shell_commands = "; ".join(dependency_shell_commands)
                     command = "%s; %s" % (dependency_shell_commands, command)
diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index 18fdd813f66..c4c00b3ef9d 100755
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -1252,13 +1252,14 @@ class Tool( object, Dictifiable ):
         visit_input_values( self.inputs, values, validate_inputs )
         return messages
 
-    def build_dependency_shell_commands( self, job_directory=None ):
+    def build_dependency_shell_commands( self, job_directory=None, metadata=False ):
         """Return a list of commands to be run to populate the current environment to include this tools requirements."""
         return self.app.toolbox.dependency_manager.dependency_shell_commands(
             self.requirements,
             installed_tool_dependencies=self.installed_tool_dependencies,
             tool_dir=self.tool_dir,
             job_directory=job_directory,
+            metadata=metadata,
         )
 
     @property
diff --git a/lib/galaxy/tools/deps/resolvers/conda.py b/lib/galaxy/tools/deps/resolvers/conda.py
index e2ac9c69d58..625a11089d3 100644
--- a/lib/galaxy/tools/deps/resolvers/conda.py
+++ b/lib/galaxy/tools/deps/resolvers/conda.py
@@ -125,7 +125,12 @@ class CondaDependencyResolver(DependencyResolver, ListableDependencyResolver, In
             return INDETERMINATE_DEPENDENCY
 
         # Have installed conda_target and job_directory to send it too.
-        conda_environment = os.path.join(job_directory, "conda-env")
+        # If dependency is for metadata generation, store environment in conda-metadata-env
+        if kwds.get("metadata", False):
+            conda_env = "conda-metadata-env"
+        else:
+            conda_env = "conda-env"
+        conda_environment = os.path.join(job_directory, conda_env)
         env_path, exit_code = build_isolated_environment(
             conda_target,
             path=conda_environment,