diff --git a/src/pyff/builtins.py b/src/pyff/builtins.py
index a3a69ae2..89b623fb 100644
--- a/src/pyff/builtins.py
+++ b/src/pyff/builtins.py
@@ -552,10 +552,6 @@ def _nop(x):
     out = output_file
     data = req.t
 
-    # clean unused namespaces - the working document isn't always XML (eg discojson* produce JSON)
-    if isinstance(data, (etree._Element, etree._ElementTree)):
-        etree.cleanup_namespaces(data)
-
     if not req.args.get('raw'):
         data = dumptree(req.t, pretty_print=req.args.get('pretty_print'))
 
diff --git a/src/pyff/samlmd.py b/src/pyff/samlmd.py
index b23f41b4..ae00ce6b 100644
--- a/src/pyff/samlmd.py
+++ b/src/pyff/samlmd.py
@@ -488,6 +488,12 @@ def entitiesdescriptor(
             ent_insert = deepcopy(ent_insert)
         t.append(ent_insert)
 
+    # clean unused namespaces
+    # Keep xs: and xsi:, as these are crucial - and xs: is used only
+    # in attribute values, so may appear as unused.
+    keep_ns_prefixes = ['xs', 'xsi']
+    etree.cleanup_namespaces(t, keep_ns_prefixes=keep_ns_prefixes)
+
     if config.devel_write_xml_to_file:
         import os