diff --git a/core/dbt/task/clean.py b/core/dbt/task/clean.py
index 8632c6e29e2..b058507153a 100644
--- a/core/dbt/task/clean.py
+++ b/core/dbt/task/clean.py
@@ -2,7 +2,7 @@
 import os
 import shutil
 
-from dbt.task.base import BaseTask
+from dbt.task.base import BaseTask, move_to_nearest_project_dir
 from dbt.logger import GLOBAL_LOGGER as logger
 from dbt.config import UnsetProfileConfig
 
@@ -32,6 +32,7 @@ def run(self):
         This function takes all the paths in the target file
         and cleans the project paths that are not protected.
         """
+        move_to_nearest_project_dir(self.args)
         for path in self.config.clean_targets:
             logger.info("Checking {}/*".format(path))
             if not self.__is_protected_path(path):
diff --git a/test/integration/015_cli_invocation_tests/test_cli_invocation.py b/test/integration/015_cli_invocation_tests/test_cli_invocation.py
index 72c76846b24..270d5a73fef 100644
--- a/test/integration/015_cli_invocation_tests/test_cli_invocation.py
+++ b/test/integration/015_cli_invocation_tests/test_cli_invocation.py
@@ -168,3 +168,4 @@ def _run_simple_dbt_commands(self, project_dir):
         self.run_dbt(['seed', '--project-dir', project_dir])
         self.run_dbt(['run', '--project-dir', project_dir])
         self.run_dbt(['test', '--project-dir', project_dir])
+        self.run_dbt(['clean', '--project-dir', project_dir])