diff --git a/spacy/vocab.pyx b/spacy/vocab.pyx
index 1b1b04e13..3617e70bb 100644
--- a/spacy/vocab.pyx
+++ b/spacy/vocab.pyx
@@ -316,6 +316,9 @@ cdef class Vocab:
         DOCS: https://spacy.io/api/vocab#prune_vectors
         """
         xp = get_array_module(self.vectors.data)
+        # Make sure all vectors are in the vocab
+        for orth in self.vectors:
+            self[orth]
         # Make prob negative so it sorts by rank ascending
         # (key2row contains the rank)
         priority = [(-lex.prob, self.vectors.key2row[lex.orth], lex.orth)