diff --git a/Framework/PythonInterface/mantid/__init__.py b/Framework/PythonInterface/mantid/__init__.py
index 1e756bc460ef..b76a24c27754 100644
--- a/Framework/PythonInterface/mantid/__init__.py
+++ b/Framework/PythonInterface/mantid/__init__.py
@@ -48,7 +48,8 @@ def apiVersion():
 ###############################################################################
 import warnings as _warnings
 # Default we see everything
-_warnings.filterwarnings("default",category=DeprecationWarning)
+_warnings.filterwarnings("default",category=DeprecationWarning,
+                         module="mantid.*")
 # We can't do anything about numpy.oldnumeric being deprecated but
 # still used in other libraries, e.g scipy, so just ignore those
 _warnings.filterwarnings("ignore",category=DeprecationWarning,
diff --git a/MantidPlot/ipython_widget/mantid_ipython_widget.py b/MantidPlot/ipython_widget/mantid_ipython_widget.py
index 0ac7c5557306..344828b31860 100644
--- a/MantidPlot/ipython_widget/mantid_ipython_widget.py
+++ b/MantidPlot/ipython_widget/mantid_ipython_widget.py
@@ -4,6 +4,7 @@
 import inspect
 import threading
 import types
+import warnings
 
 from PyQt4 import QtGui
 
@@ -14,8 +15,20 @@
 # Monkeypatch!
 RegexLexer.get_tokens_unprocessed_unpatched = RegexLexer.get_tokens_unprocessed
 
-from IPython.qt.console.rich_ipython_widget import RichIPythonWidget
-from IPython.qt.inprocess import QtInProcessKernelManager
+# Ignore Jupyter/IPython deprecation warnings that we can't do anything about
+warnings.filterwarnings('ignore', category=DeprecationWarning, module='IPython.*')
+warnings.filterwarnings('ignore', category=DeprecationWarning, module='ipykernel.*')
+warnings.filterwarnings('ignore', category=DeprecationWarning, module='jupyter_client.*')
+warnings.filterwarnings('ignore', category=DeprecationWarning, module='qtconsole.*')
+del warnings
+
+try:
+    # Later versions of Qtconsole are part of Jupyter
+    from qtconsole.rich_jupyter_widget import RichJupyterWidget as RichIPythonWidget
+    from qtconsole.inprocess import QtInProcessKernelManager
+except ImportError:
+    from IPython.qt.console.rich_ipython_widget import RichIPythonWidget
+    from IPython.qt.inprocess import QtInProcessKernelManager
 
 def our_run_code(self, code_obj, result=None):
     """ Method with which we replace the run_code method of IPython's InteractiveShell class.