diff --git a/ycmd/completers/language_server/language_server_completer.py b/ycmd/completers/language_server/language_server_completer.py
index 8f3e30e552..8ccf37c73c 100644
--- a/ycmd/completers/language_server/language_server_completer.py
+++ b/ycmd/completers/language_server/language_server_completer.py
@@ -1283,12 +1283,18 @@ def GetSettings( self, module, request_data ):
 
 
   def _GetSettingsFromExtraConf( self, request_data ):
-    self._settings = self.DefaultSettings( request_data )
+    ls = self.DefaultSettings( request_data )
+    # In case no module is found
+    self._settings = {
+      'ls': ls
+    }
 
     module = extra_conf_store.ModuleForSourceFile( request_data[ 'filepath' ] )
     if module:
-      settings = self.GetSettings( module, request_data )
-      self._settings.update( settings.get( 'ls', {} ) )
+      self._settings = self.GetSettings( module, request_data )
+      ls.update( self._settings.get( 'ls', {} ) )
+      self._settings[ 'ls' ] = ls
+
       # Only return the dir if it was found in the paths; we don't want to use
       # the path of the global extra conf as a project root dir.
       if not extra_conf_store.IsGlobalExtraConfModule( module ):
@@ -1706,7 +1712,8 @@ def _SendInitialize( self, request_data, extra_conf_dir ):
       # clear how/where that is specified.
       msg = lsp.Initialize( request_id,
                             self._project_directory,
-                            self._settings )
+                            self._settings.get( 'ls', {} ),
+                            self._settings.get( 'capabilities', {} ) )
 
       def response_handler( response, message ):
         if message is None:
@@ -1819,7 +1826,7 @@ def _HandleInitializeInPollThread( self, response ):
       # configuration should be send in response to a workspace/configuration
       # request?
       self.GetConnection().SendNotification(
-          lsp.DidChangeConfiguration( self._settings ) )
+          lsp.DidChangeConfiguration( self._settings.get( 'ls', {} ) ) )
 
       # Notify the other threads that we have completed the initialize exchange.
       self._initialize_response = None
diff --git a/ycmd/completers/language_server/language_server_protocol.py b/ycmd/completers/language_server/language_server_protocol.py
index 601bef3e55..8710f0b200 100644
--- a/ycmd/completers/language_server/language_server_protocol.py
+++ b/ycmd/completers/language_server/language_server_protocol.py
@@ -34,7 +34,8 @@
                          unquote,
                          url2pathname,
                          urlparse,
-                         urljoin )
+                         urljoin,
+                         UpdateDict )
 
 
 Error = collections.namedtuple( 'RequestError', [ 'code', 'reason' ] )
@@ -233,7 +234,10 @@ def BuildResponse( request, parameters ):
   return _BuildMessageData( message )
 
 
-def Initialize( request_id, project_directory, settings ):
+def Initialize( request_id,
+                project_directory,
+                settings,
+                capabilities ):
   """Build the Language Server initialize request"""
 
   return BuildRequest( request_id, 'initialize', {
@@ -241,8 +245,11 @@ def Initialize( request_id, project_directory, settings ):
     'rootPath': project_directory,
     'rootUri': FilePathToUri( project_directory ),
     'initializationOptions': settings,
-    'capabilities': {
-      'workspace': { 'applyEdit': True, 'documentChanges': True },
+    'capabilities': UpdateDict( {
+      'workspace': {
+          'applyEdit': True,
+          'documentChanges': True,
+      },
       'textDocument': {
         'codeAction': {
           'codeActionLiteralSupport': {
@@ -288,7 +295,7 @@ def Initialize( request_id, project_directory, settings ):
           },
         },
       },
-    },
+    }, capabilities ),
   } )
 
 
diff --git a/ycmd/utils.py b/ycmd/utils.py
index fca525fbb1..90aed0564b 100644
--- a/ycmd/utils.py
+++ b/ycmd/utils.py
@@ -24,7 +24,12 @@
 # Not installing aliases from python-future; it's unreliable and slow.
 from builtins import *  # noqa
 
-from future.utils import PY2, native
+try:
+  import collections.abc as collections_abc
+except ImportError:
+  import collections as collections_abc
+
+from future.utils import PY2, native, iteritems
 import copy
 import json
 import logging
@@ -673,3 +678,46 @@ def GetClangResourceDir():
 
 
 CLANG_RESOURCE_DIR = GetClangResourceDir()
+
+
+def UpdateDict( target, override ):
+  """Apply the updates in |override| to the dict |target|. This is like
+  dict.update, but recursive. i.e. if the existing element is a dict, then
+  override elements of the sub-dict rather than wholesale replacing.
+
+  e.g. 
+
+  UpdateDict(
+    {
+      'outer': { 'inner': { 'key': 'oldValue', 'existingKey': True } }
+    },
+    {
+      'outer': { 'inner': { 'key': 'newValue' } },
+      'newKey': { 'newDict': True },
+    }
+  )
+
+  yields:
+
+    {
+      outer: {
+        inner: {
+           key: 'newValue',
+           exitingKey: True
+        }
+      },
+      newKey: { newDict: True }
+    }
+
+  """
+  
+  for key, value in iteritems( override ):
+    current_value = target.get( key )
+    if not isinstance( current_value, collections_abc.Mapping ):
+      target[ key ] = value
+    elif isinstance( value, collections_abc.Mapping ):
+      target[ key ] = UpdateDict( current_value, value )
+    else:
+      target[ key ] = value
+
+  return target