diff --git a/sphinx/builders/__init__.py b/sphinx/builders/__init__.py
index 9dc757cd4..6230502d1 100644
--- a/sphinx/builders/__init__.py
+++ b/sphinx/builders/__init__.py
@@ -287,7 +287,7 @@ class Builder(object):
             logger.info(bold('building [%s]' % self.name) + ': ' + summary)
 
         # while reading, collect all warnings from docutils
-        with logging.pending_logging():
+        with logging.pending_warnings():
             updated_docnames = set(self.env.update(self.config, self.srcdir,
                                                    self.doctreedir, self.app))
 
@@ -386,7 +386,7 @@ class Builder(object):
 
     def _write_serial(self, docnames):
         # type: (Sequence[unicode]) -> None
-        with logging.pending_logging():
+        with logging.pending_warnings():
             for docname in self.app.status_iterator(
                     docnames, 'writing output... ', darkgreen, len(docnames)):
                 doctree = self.env.get_and_resolve_doctree(docname, self)
diff --git a/sphinx/util/logging.py b/sphinx/util/logging.py
index 7afaadf34..a473ffc97 100644
--- a/sphinx/util/logging.py
+++ b/sphinx/util/logging.py
@@ -126,6 +126,11 @@ class SphinxLoggerAdapter(logging.LoggerAdapter):
         self.logger.handle(record)  # type: ignore
 
 
+class WarningStreamHandler(logging.StreamHandler):
+    """StreamHandler for warnings."""
+    pass
+
+
 class NewLineStreamHandlerPY2(logging.StreamHandler):
     """StreamHandler which switches line terminator by record.nonl flag."""
 
@@ -195,10 +200,36 @@ class MemoryHandler(logging.handlers.BufferingHandler):
         return buffer
 
 
+@contextmanager
+def pending_warnings():
+    # type: () -> Generator
+    """contextmanager to pend logging warnings temporary."""
+    logger = logging.getLogger()
+    memhandler = MemoryHandler()
+    memhandler.setLevel(logging.WARNING)
+
+    try:
+        handlers = []
+        for handler in logger.handlers[:]:
+            if isinstance(handler, WarningStreamHandler):
+                logger.removeHandler(handler)
+                handlers.append(handler)
+
+        logger.addHandler(memhandler)
+        yield memhandler
+    finally:
+        logger.removeHandler(memhandler)
+
+        for handler in handlers:
+            logger.addHandler(handler)
+
+        memhandler.flushTo(logger)
+
+
 @contextmanager
 def pending_logging():
     # type: () -> Generator
-    """contextmanager to pend logging temporary."""
+    """contextmanager to pend logging all logs temporary."""
     logger = logging.getLogger()
     memhandler = MemoryHandler()
 
@@ -357,7 +388,7 @@ def setup(app, status, warning):
     info_handler.setLevel(VERBOSITY_MAP.get(app.verbosity))
     info_handler.setFormatter(ColorizeFormatter())
 
-    warning_handler = logging.StreamHandler(warning)
+    warning_handler = WarningStreamHandler(warning)
     warning_handler.addFilter(WarningSuppressor(app))
     warning_handler.addFilter(WarningIsErrorFilter(app))
     warning_handler.addFilter(WarningLogRecordTranslator(app))
diff --git a/tests/test_util_logging.py b/tests/test_util_logging.py
index 25816bf4e..984b52220 100644
--- a/tests/test_util_logging.py
+++ b/tests/test_util_logging.py
@@ -225,12 +225,12 @@ def test_warn_node(app, status, warning):
 
 
 @with_app()
-def test_pending_logging(app, status, warning):
+def test_pending_warnings(app, status, warning):
     logging.setup(app, status, warning)
     logger = logging.getLogger(__name__)
 
     logger.warning('message1')
-    with logging.pending_logging():
+    with logging.pending_warnings():
         # not logged yet (bufferred) in here
         logger.warning('message2')
         logger.warning('message3')