diff --git a/spacy/tokens/doc.pyx b/spacy/tokens/doc.pyx
index 52abf47c0..66759d271 100644
--- a/spacy/tokens/doc.pyx
+++ b/spacy/tokens/doc.pyx
@@ -323,7 +323,10 @@ cdef class Doc:
             cdef int i
             for i in range(self.length):
                 self.c[i].ent_type = 0
-                self.c[i].ent_iob = 2 # Means O, not missing!
+                # At this point we don't know whether the NER has run over the 
+                # Doc. If the ent_iob is missing, leave it missing.
+                if self.c[i].ent_iob != 0:
+                    self.c[i].ent_iob = 2 # Means O. Non-O are set from ents.
             cdef attr_t ent_type
             cdef int start, end
             for ent_info in ents: