diff --git a/spacy/pipeline/entity_linker.py b/spacy/pipeline/entity_linker.py
index 3f70475fd40..0581d51ab23 100644
--- a/spacy/pipeline/entity_linker.py
+++ b/spacy/pipeline/entity_linker.py
@@ -284,9 +284,11 @@ def initialize(
         nO = self.kb.entity_vector_length
         doc_sample = []
         vector_sample = []
+        orig_ents = []
         for eg in islice(get_examples(), 10):
             doc = eg.x
             if self.use_gold_ents:
+                orig_ents.append(doc.ents)
                 ents, _ = eg.get_aligned_ents_and_ner()
                 doc.ents = ents
             doc_sample.append(doc)
@@ -313,6 +315,10 @@ def initialize(
         if not has_annotations:
             # Clean up dummy annotation
             doc.ents = []
+        if self.use_gold_ents:
+            assert len(doc_sample) == len(orig_ents)
+            for doc, orig_ent in zip(doc_sample, orig_ents):
+                doc.ents = orig_ent
 
     def batch_has_learnable_example(self, examples):
         """Check if a batch contains a learnable example.