diff --git a/lib/galaxy/jobs/command_factory.py b/lib/galaxy/jobs/command_factory.py
index 848214a7dd2a..548c7d4dff33 100644
--- a/lib/galaxy/jobs/command_factory.py
+++ b/lib/galaxy/jobs/command_factory.py
@@ -15,6 +15,7 @@
 log = getLogger(__name__)
 
 CAPTURE_RETURN_CODE = "return_code=$?"
+YIELD_CAPTURED_CODE = 'sh -c "exit $return_code"'
 SETUP_GALAXY_FOR_METADATA = """
 [ "$GALAXY_VIRTUAL_ENV" = "None" ] && GALAXY_VIRTUAL_ENV="$_GALAXY_VIRTUAL_ENV"; _galaxy_setup_environment True
 """
@@ -268,6 +269,8 @@ def capture_return_code(self):
             self.append_command(CAPTURE_RETURN_CODE)
 
     def build(self):
+        if self.return_code_captured:
+            self.append_command(YIELD_CAPTURED_CODE)
         return self.commands
 
 
diff --git a/lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh b/lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh
index 927b9c5f1de0..81107c568b58 100644
--- a/lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh
+++ b/lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh
@@ -37,7 +37,5 @@ cd $working_directory
 $memory_statement
 $instrument_pre_commands
 $command
-echo $return_code > $exit_code_path
+echo $? > $exit_code_path
 $instrument_post_commands
-# exit with the exit code captured for the tool_script
-sh -c "exit $return_code"
diff --git a/lib/galaxy/jobs/runners/util/job_script/__init__.py b/lib/galaxy/jobs/runners/util/job_script/__init__.py
index 4972a06d3b2d..ac557454f393 100644
--- a/lib/galaxy/jobs/runners/util/job_script/__init__.py
+++ b/lib/galaxy/jobs/runners/util/job_script/__init__.py
@@ -67,7 +67,7 @@ def job_script(template=DEFAULT_JOB_FILE_TEMPLATE, **kwds):
     >>> script = job_script(working_directory='wd', command='uptime', exit_code_path='ec')
     >>> '\\nuptime\\n' in script
     True
-    >>> 'echo $return_code > ec' in script
+    >>> 'echo $? > ec' in script
     True
     >>> 'GALAXY_LIB="None"' in script
     True
diff --git a/test/unit/jobs/test_command_factory.py b/test/unit/jobs/test_command_factory.py
index 79835095c08a..e1f533495ebc 100644
--- a/test/unit/jobs/test_command_factory.py
+++ b/test/unit/jobs/test_command_factory.py
@@ -32,49 +32,49 @@ def tearDown(self):
 
     def test_simplest_command(self):
         self.include_work_dir_outputs = False
-        self.__assert_command_is(_surround_command(MOCK_COMMAND_LINE + "; return_code=$?"))
+        self.__assert_command_is(_surrond_command(MOCK_COMMAND_LINE + "; return_code=$?"))
 
     def test_shell_commands(self):
         self.include_work_dir_outputs = False
         dep_commands = [". /opt/galaxy/tools/bowtie/default/env.sh"]
         self.job_wrapper.dependency_shell_commands = dep_commands
-        self.__assert_command_is(_surround_command("%s; %s; return_code=$?" % (dep_commands[0], MOCK_COMMAND_LINE)))
+        self.__assert_command_is(_surrond_command("%s; %s; return_code=$?" % (dep_commands[0], MOCK_COMMAND_LINE)))
 
     def test_shell_commands_external(self):
         self.job_wrapper.commands_in_new_shell = True
         self.include_work_dir_outputs = False
         dep_commands = [". /opt/galaxy/tools/bowtie/default/env.sh"]
         self.job_wrapper.dependency_shell_commands = dep_commands
-        self.__assert_command_is(_surround_command("%s/tool_script.sh; return_code=$?" % self.job_wrapper.working_directory))
+        self.__assert_command_is(_surrond_command("%s/tool_script.sh; return_code=$?" % self.job_wrapper.working_directory))
         self.__assert_tool_script_is("#!/bin/sh\n%s; %s" % (dep_commands[0], MOCK_COMMAND_LINE))
 
     def test_remote_dependency_resolution(self):
         self.include_work_dir_outputs = False
         dep_commands = [". /opt/galaxy/tools/bowtie/default/env.sh"]
         self.job_wrapper.dependency_shell_commands = dep_commands
-        self.__assert_command_is(_surround_command(MOCK_COMMAND_LINE + "; return_code=$?"), remote_command_params=dict(dependency_resolution="remote"))
+        self.__assert_command_is(_surrond_command(MOCK_COMMAND_LINE + "; return_code=$?"), remote_command_params=dict(dependency_resolution="remote"))
 
     def test_explicit_local_dependency_resolution(self):
         self.include_work_dir_outputs = False
         dep_commands = [". /opt/galaxy/tools/bowtie/default/env.sh"]
         self.job_wrapper.dependency_shell_commands = dep_commands
-        self.__assert_command_is(_surround_command("%s; %s; return_code=$?" % (dep_commands[0], MOCK_COMMAND_LINE)),
+        self.__assert_command_is(_surrond_command("%s; %s; return_code=$?" % (dep_commands[0], MOCK_COMMAND_LINE)),
                                  remote_command_params=dict(dependency_resolution="local"))
 
     def test_task_prepare_inputs(self):
         self.include_work_dir_outputs = False
         self.job_wrapper.prepare_input_files_cmds = ["/opt/split1", "/opt/split2"]
-        self.__assert_command_is(_surround_command("/opt/split1; /opt/split2; %s; return_code=$?") % MOCK_COMMAND_LINE)
+        self.__assert_command_is(_surrond_command("/opt/split1; /opt/split2; %s; return_code=$?") % MOCK_COMMAND_LINE)
 
     def test_workdir_outputs(self):
         self.include_work_dir_outputs = True
         self.workdir_outputs = [("foo", "bar")]
-        self.__assert_command_is(_surround_command('%s; return_code=$?; if [ -f foo ] ; then cp foo bar ; fi' % MOCK_COMMAND_LINE))
+        self.__assert_command_is(_surrond_command('%s; return_code=$?; if [ -f foo ] ; then cp foo bar ; fi' % MOCK_COMMAND_LINE))
 
     def test_set_metadata_skipped_if_unneeded(self):
         self.include_metadata = True
         self.include_work_dir_outputs = False
-        self.__assert_command_is(_surround_command(MOCK_COMMAND_LINE + "; return_code=$?"))
+        self.__assert_command_is(_surrond_command(MOCK_COMMAND_LINE + "; return_code=$?"))
 
     def test_set_metadata(self):
         self._test_set_metadata()
@@ -87,7 +87,7 @@ def _test_set_metadata(self):
         self.include_metadata = True
         self.include_work_dir_outputs = False
         self.job_wrapper.metadata_line = TEST_METADATA_LINE
-        expected_command = _surround_command("%s; return_code=$?; cd '%s'; %s%s" % (MOCK_COMMAND_LINE, self.job_dir, SETUP_GALAXY_FOR_METADATA, TEST_METADATA_LINE))
+        expected_command = _surrond_command("%s; return_code=$?; cd '%s'; %s%s" % (MOCK_COMMAND_LINE, self.job_dir, SETUP_GALAXY_FOR_METADATA, TEST_METADATA_LINE))
         self.__assert_command_is(expected_command)
 
     def test_empty_metadata(self):
@@ -98,7 +98,7 @@ def test_empty_metadata(self):
         self.include_work_dir_outputs = False
         self.job_wrapper.metadata_line = ' '
         # Empty metadata command do not touch command line.
-        expected_command = _surround_command("%s; return_code=$?; cd '%s'" % (MOCK_COMMAND_LINE, self.job_dir))
+        expected_command = _surrond_command("%s; return_code=$?; cd '%s'" % (MOCK_COMMAND_LINE, self.job_dir))
         self.__assert_command_is(expected_command)
 
     def test_metadata_kwd_defaults(self):
@@ -152,8 +152,8 @@ def __command(self, **extra_kwds):
         return build_command(**kwds)
 
 
-def _surround_command(command):
-    return '''rm -rf working; mkdir -p working; cd working; %s''' % command
+def _surrond_command(command):
+    return '''rm -rf working; mkdir -p working; cd working; %s; sh -c "exit $return_code"''' % command
 
 
 class MockJobWrapper(object):