diff --git a/lib/galaxy/app.py b/lib/galaxy/app.py
index a8b2c79e9b7..84be1d207cc 100644
--- a/lib/galaxy/app.py
+++ b/lib/galaxy/app.py
@@ -212,12 +212,10 @@ class UniverseApplication(object, config.ConfiguresGalaxyMixin):
 
         self.model.engine.dispose()
         self.server_starttime = int(time.time())  # used for cachebusting
-        # When running the application without a web stack, exit == True signals the application loop to break and call
-        # the shutdown method
-        self.exit = False
         log.info("Galaxy app startup finished %s" % self.startup_timer)
 
     def shutdown(self):
+        log.debug('Shutting down')
         exception = None
         try:
             self.watchers.shutdown()
@@ -263,12 +261,17 @@ class UniverseApplication(object, config.ConfiguresGalaxyMixin):
             exception = exception or e
             log.exception("Failed to shutdown SA database engine cleanly")
 
-        self.application_stack.shutdown()
-        # This is used to signal the webless application loop to terminate
-        self.exit = True
+        try:
+            self.application_stack.shutdown()
+        except Exception as e:
+            exception = exception or e
+            log.exception("Failed to shutdown application stack interface cleanly")
 
         if exception:
             raise exception
+        else:
+            log.debug('Finished shutting down')
+
 
     def configure_fluent_log(self):
         if self.config.fluent_log:
diff --git a/lib/galaxy/web/stack/__init__.py b/lib/galaxy/web/stack/__init__.py
index 5f0d71bebda..7476afec21b 100644
--- a/lib/galaxy/web/stack/__init__.py
+++ b/lib/galaxy/web/stack/__init__.py
@@ -5,7 +5,6 @@ from __future__ import absolute_import
 import inspect
 import logging
 import os
-import signal
 
 # The uwsgi module is automatically injected by the parent uwsgi
 # process and only exists that way.  If anything works, this is a
@@ -210,21 +209,6 @@ class UWSGIApplicationStack(MessageApplicationStack):
         self._mules_list = None
         super(UWSGIApplicationStack, self).__init__(app=app, config=config)
 
-    def __register_signal_handlers(self):
-        for name in ('TERM', 'INT', 'HUP'):
-            sig = getattr(signal, 'SIG%s' % name)
-            signal.signal(sig, self._handle_signal)
-
-    def _handle_signal(self, signum, frame):
-        # uWSGI always sends SIGINT even if the master received SIGTERM
-        if signum in (signal.SIGTERM, signal.SIGINT):
-            log.info('Received SIGTERM/SIGINT, shutting down gracefully')
-        elif signum == signal.SIGHUP:
-            log.debug('Received SIGHUP, restarting')
-        self.shutdown()
-        # this terminates the application loop in the mule script, in the case of HUP, uWSGI will restart the mule
-        self.app.exit = True
-
     @property
     def _configured_mules(self):
         if self._mules_list is None:
diff --git a/scripts/galaxy-main b/scripts/galaxy-main
index 4c82e41ecfb..8e3fea4f83f 100755
--- a/scripts/galaxy-main
+++ b/scripts/galaxy-main
@@ -25,7 +25,9 @@ The --py-call-osafterfork allows for proper shutdown on SIGTERM/SIGINT.
 import functools
 import logging
 import os
+import signal
 import sys
+import threading
 import time
 from argparse import ArgumentParser
 from logging.config import fileConfig
@@ -55,6 +57,10 @@ DEFAULT_PID = "galaxy.pid"
 DEFAULT_VERBOSE = True
 DESCRIPTION = "Daemonized entry point for Galaxy."
 
+SHUTDOWN_MSG = '__SHUTDOWN__'
+
+exit = threading.Event()
+
 
 def load_galaxy_app(
     config_builder,
@@ -88,6 +94,17 @@ def load_galaxy_app(
     return app
 
 
+def handle_signal(signum, frame):
+    log.info('Received signal %d, exiting', signum)
+    exit.set()
+
+
+def register_signals():
+    for name in ('TERM', 'INT', 'HUP'):
+        sig = getattr(signal, 'SIG%s' % name)
+        signal.signal(sig, handle_signal)
+
+
 def app_loop(args, log):
     try:
         config_builder = GalaxyConfigBuilder(args)
@@ -99,15 +116,12 @@ def app_loop(args, log):
     except BaseException:
         log.exception("Failed to initialize Galaxy application")
         raise
-    while not galaxy_app.exit:
-        try:
-            time.sleep(5)
-        except KeyboardInterrupt:
-            galaxy_app.exit = True
-        except SystemExit:
-            galaxy_app.exit = True
-        except Exception:
+    try:
+        # A timeout is required or the signals won't be handled
+        while not exit.wait(20):
             pass
+    except (KeyboardInterrupt, SystemExit):
+        pass
     try:
         galaxy_app.shutdown()
     except Exception:
@@ -221,6 +235,7 @@ def main():
 
     log.setLevel(logging.DEBUG)
     log.propagate = False
+    register_signals()
     if args.daemonize:
         if Daemonize is None:
             raise ImportError(REQUIRES_DAEMONIZE_MESSAGE)