diff --git a/doc/build_extension_docs.py b/doc/build_extension_docs.py
index bee61cdd..f0569d0a 100755
--- a/doc/build_extension_docs.py
+++ b/doc/build_extension_docs.py
@@ -17,6 +17,7 @@
 
 import os
 import sys
+import shutil
 
 from wlauto import ExtensionLoader
 from wlauto.utils.doc import get_rst_from_extension, underline
@@ -30,6 +31,9 @@ def generate_extension_documentation(source_dir, outdir, ignore_paths):
     loader = ExtensionLoader(keep_going=True)
     loader.clear()
     loader.update(paths=[source_dir], ignore_paths=ignore_paths)
+    if os.path.exists(outdir):
+        shutil.rmtree(outdir)
+    os.makedirs(outdir)
     for ext_type in loader.extension_kinds:
         if not ext_type in GENERATE_FOR:
             continue
diff --git a/doc/build_instrumentation_method_map.py b/doc/build_instrumentation_method_map.py
index a9438c92..7dc61c92 100755
--- a/doc/build_instrumentation_method_map.py
+++ b/doc/build_instrumentation_method_map.py
@@ -38,6 +38,8 @@ def generate_instrumentation_method_map(outfile):
                                        headers=['method name', 'signal'], align='<<')
     priority_table = format_simple_table([(escape_trailing_underscore(k), v)  for k, v in PRIORITY_MAP.iteritems()],
                                          headers=['prefix', 'priority'],  align='<>')
+    if os.path.isfile(outfile):
+        os.unlink(outfile)
     with open(OUTPUT_TEMPLATE_FILE) as fh:
         template = string.Template(fh.read())
     with open(outfile, 'w') as wfh: