diff --git a/Framework/PythonInterface/plugins/algorithms/AlignAndFocusPowderFromFiles.py b/Framework/PythonInterface/plugins/algorithms/AlignAndFocusPowderFromFiles.py
index 899e90b644172f321a87d6db9c3acfb4d4b0d465..4208524c848c246d2b225f8be52659d7d7bf5d11 100644
--- a/Framework/PythonInterface/plugins/algorithms/AlignAndFocusPowderFromFiles.py
+++ b/Framework/PythonInterface/plugins/algorithms/AlignAndFocusPowderFromFiles.py
@@ -230,6 +230,10 @@ class AlignAndFocusPowderFromFiles(DataProcessorAlgorithm):
                 if self.kwargs['PreserveEvents']:
                     CompressEvents(InputWorkspace=finalname, OutputWorkspace=finalname)
 
+        # with more than one chunk or file the integrated proton charge is
+        # generically wrong
+        mtd[finalname].integrateProtonCharge()
+
         # set the output workspace
         self.setProperty('OutputWorkspace', mtd[finalname])