diff --git a/config/galaxy.ini.sample b/config/galaxy.ini.sample
index f8b80f362ef..b590b8a589c 100644
--- a/config/galaxy.ini.sample
+++ b/config/galaxy.ini.sample
@@ -206,7 +206,7 @@ paste.app_factory = galaxy.web.buildapp:app_factory
 #conda_verbose_install_check=False
 # Set to True to instruct Galaxy to install Conda from the web automatically
 # if it cannot find a local copy and conda_exec is not configured.
-#conda_auto_init = True
+#conda_auto_init = False
 
 # File containing the Galaxy Tool Sheds that should be made available to
 # install from in the admin interface (.sample used if default does not exist).
diff --git a/doc/source/releases/16.07.rst b/doc/source/releases/16.07.rst
index 7ff2fe2b070..35a2577dcd7 100644
--- a/doc/source/releases/16.07.rst
+++ b/doc/source/releases/16.07.rst
@@ -5,6 +5,8 @@
 16.07
 -------------------------------
 
+.. announce_start
+
 Highlighted Enhancements
 -------------------------------
 
diff --git a/lib/galaxy/tools/deps/__init__.py b/lib/galaxy/tools/deps/__init__.py
index 65971dfc825..f7afa8e8a65 100644
--- a/lib/galaxy/tools/deps/__init__.py
+++ b/lib/galaxy/tools/deps/__init__.py
@@ -22,7 +22,7 @@ EXTRA_CONFIG_KWDS = {
     'conda_debug': None,
     'conda_ensure_channels': 'r,bioconda,iuc',
     'conda_auto_install': False,
-    'conda_auto_init': True,
+    'conda_auto_init': False,
 }
 
 CONFIG_VAL_NOT_FOUND = object()
diff --git a/lib/galaxy/tools/deps/resolvers/conda.py b/lib/galaxy/tools/deps/resolvers/conda.py
index 6f9f64e0dd7..d2ff051477e 100644
--- a/lib/galaxy/tools/deps/resolvers/conda.py
+++ b/lib/galaxy/tools/deps/resolvers/conda.py
@@ -56,6 +56,8 @@ class CondaDependencyResolver(DependencyResolver, ListableDependencyResolver, In
                 dependency_manager.default_base_path, DEFAULT_BASE_PATH_DIRECTORY
             )
 
+        self.conda_prefix_parent = os.path.dirname(conda_prefix)
+
         # warning is related to conda problem discussed in https://github.com/galaxyproject/galaxy/issues/2537, remove when that is resolved
         conda_prefix_warning_length = 50
         if len(conda_prefix) >= conda_prefix_warning_length:
@@ -104,21 +106,31 @@ class CondaDependencyResolver(DependencyResolver, ListableDependencyResolver, In
         Make sure that conda is installed, and if conda can't be installed, mark resolver as disabled.
         We acquire a lock, so that multiple handlers do not attempt to install conda simultaneously.
         """
-        if not os.path.exists(self.dependency_manager.default_base_path):
-            os.mkdir(self.dependency_manager.default_base_path)
-        try:
-            with FileLock(os.path.join(self.dependency_manager.default_base_path, 'conda')):
-                if not self.conda_context.is_conda_installed():
-                    if self.auto_init:
-                        if self.conda_context.can_install_conda():
-                            if install_conda(self.conda_context):
-                                self.disabled = True
-                                log.warning("Conda installation requested and failed.")
-                        else:
+        target_path = self.conda_prefix_parent
+
+        def _check():
+            if not self.conda_context.is_conda_installed():
+                if self.auto_init:
+                    if self.conda_context.can_install_conda():
+                        if install_conda(self.conda_context):
                             self.disabled = True
+                            log.warning("Conda installation requested and failed.")
                     else:
                         self.disabled = True
-                        log.warning("Conda not installed and auto-installation disabled.")
+                else:
+                    self.disabled = True
+                    log.warning("Conda not installed and auto-installation disabled.")
+            else:
+                self.disabled = False
+
+        if not os.path.exists(target_path):
+            os.mkdir(target_path)
+        try:
+            if self.auto_init and os.access(target_path, os.W_OK):
+                with FileLock(os.path.join(target_path, 'conda')):
+                    _check()
+            else:
+                _check()
         except FileLockException:
             self.ensure_conda_installed()
 
diff --git a/lib/galaxy/tools/toolbox/base.py b/lib/galaxy/tools/toolbox/base.py
index e23d91b8732..2a2b998b253 100644
--- a/lib/galaxy/tools/toolbox/base.py
+++ b/lib/galaxy/tools/toolbox/base.py
@@ -15,7 +15,6 @@ from galaxy.util import listify
 from galaxy.util import parse_xml
 from galaxy.util import string_as_bool
 from galaxy.util.bunch import Bunch
-from galaxy.util.postfork import register_postfork_function
 
 from .parser import get_toolbox_parser, ensure_tool_conf_item
 
@@ -104,7 +103,6 @@ class AbstractToolBox( Dictifiable, ManagesIntegratedToolPanelMixin, object ):
                 self._init_tools_from_config( config_filename )
             except:
                 log.exception( "Error loading tools defined in config %s", config_filename )
-        register_postfork_function(self._tool_conf_watcher.start)
 
     def _init_tools_from_config( self, config_filename ):
         """
diff --git a/lib/galaxy/tools/toolbox/watcher.py b/lib/galaxy/tools/toolbox/watcher.py
index 8a84f91df16..f683603c0e5 100644
--- a/lib/galaxy/tools/toolbox/watcher.py
+++ b/lib/galaxy/tools/toolbox/watcher.py
@@ -74,7 +74,7 @@ class ToolConfWatcher(object):
     def start(self):
         if not self._active:
             self._active = True
-            self.thread.start()
+            register_postfork_function(self.thread.start)
 
     def shutdown(self):
         if self._active:
@@ -109,6 +109,7 @@ class ToolConfWatcher(object):
             mod_time = time.ctime(os.path.getmtime(path))
         with self._lock:
             self.paths[path] = mod_time
+        self.start()
 
     def watch_file(self, tool_conf_file):
         self.monitor(tool_conf_file)