diff --git a/pandoc_reader.py b/pandoc_reader.py
index ea4e9b7..6e39b04 100644
--- a/pandoc_reader.py
+++ b/pandoc_reader.py
@@ -60,9 +60,6 @@ class PandocReader(BaseReader):
             text = list(fp.splitlines())
 
         metadata, content = self._get_meta_and_content(text)
-        bib_dir = self.settings.get('PANDOC_BIBDIR', '')
-
-        bib_header = self.settings.get('PANDOC_BIBHEADER', None)
 
         filters = self.settings.get('PANDOC_FILTERS', [])
         extensions = self.settings.get('PANDOC_EXTENSIONS', '')
@@ -79,16 +76,19 @@ class PandocReader(BaseReader):
             pandoc_cmd.extend(["--filter", filt])
         pandoc_cmd.extend(extra_args)
 
+        bib_dir = self.settings.get('PANDOC_BIBDIR', '')
+        bib_header = self.settings.get('PANDOC_BIBHEADER', None)
         if "bibliography" in metadata.keys():
             bib_file = os.path.join(bib_dir, metadata['bibliography'])
             if not os.path.exists(bib_file):
                 raise FileNotFoundError(bib_file)
-            extra_args = extra_args + ['--bibliography={}'.format(bib_file)]
+            bib_args = ['--bibliography={}'.format(bib_file)]
 
             if bib_header is not None:
-                extra_args = extra_args + [
+                bib_args = bib_args + [
                     '--metadata=reference-section-title="{}"'.format(
                         bib_header)]
+            pandoc_cmd.extend(bib_args)
 
         proc = subprocess.Popen(
             pandoc_cmd,