diff --git a/haystack/document_store/sql.py b/haystack/document_store/sql.py
index d3763e686..a6d0c2afc 100644
--- a/haystack/document_store/sql.py
+++ b/haystack/document_store/sql.py
@@ -26,7 +26,7 @@ class DocumentORM(ORMBase):
     text = Column(String, nullable=False)
     index = Column(String, nullable=False)
 
-    meta = relationship("MetaORM", secondary="document_meta", backref="Document")
+    meta = relationship("MetaORM", backref="Document")
 
 
 class MetaORM(ORMBase):
@@ -34,15 +34,9 @@ class MetaORM(ORMBase):
 
     name = Column(String, index=True)
     value = Column(String, index=True)
-
-    documents = relationship(DocumentORM, secondary="document_meta", backref="Meta")
-
-
-class DocumentMetaORM(ORMBase):
-    __tablename__ = "document_meta"
-
     document_id = Column(String, ForeignKey("document.id"), nullable=False)
-    meta_id = Column(Integer, ForeignKey("meta.id"), nullable=False)
+
+    documents = relationship(DocumentORM, backref="Meta")
 
 
 class LabelORM(ORMBase):
@@ -88,9 +82,9 @@ class SQLDocumentStore(BaseDocumentStore):
         query = self.session.query(DocumentORM).filter_by(index=index)
 
         if filters:
+            query = query.join(MetaORM)
             for key, values in filters.items():
-                query = query.filter(DocumentORM.meta.any(MetaORM.name.in_([key])))\
-                             .filter(DocumentORM.meta.any(MetaORM.value.in_(values)))
+                query = query.filter(MetaORM.name == key, MetaORM.value.in_(values))
 
         documents = [self._convert_sql_row_to_document(row) for row in query.all()]
         return documents
@@ -148,12 +142,10 @@ class SQLDocumentStore(BaseDocumentStore):
         self.session.commit()
 
     def update_document_meta(self, id: str, meta: Dict[str, str]):
-        document = self.session.query(DocumentORM).get(id)
-        meta_orms = [
-            self._get_or_create(session=self.session, model=MetaORM, name=key, value=value)
-            for key, value in meta.items()
-        ]
-        document.meta = meta_orms
+        self.session.query(MetaORM).filter_by(document_id=id).delete()
+        meta_orms = [MetaORM(name=key, value=value, document_id=id) for key, value in meta.items()]
+        for m in meta_orms:
+            self.session.add(m)
         self.session.commit()
 
     def add_eval_data(self, filename: str, doc_index: str = "eval_document", label_index: str = "label"):
diff --git a/test/test_db.py b/test/test_db.py
index affe38071..502294fb9 100644
--- a/test/test_db.py
+++ b/test/test_db.py
@@ -15,6 +15,28 @@ def test_get_all_documents_without_filters(document_store_with_docs):
     assert {d.meta["meta_field"] for d in documents} == {"test1", "test2", "test3"}
 
 
+def test_get_all_document_filter_duplicate_value(document_store):
+    documents = [
+        Document(
+            text="Doc1",
+            meta={"f1": "0"}
+        ),
+        Document(
+            text="Doc1",
+            meta={"f1": "1", "vector_id": "0"}
+        ),
+        Document(
+            text="Doc2",
+            meta={"f3": "0"}
+        )
+    ]
+    document_store.write_documents(documents)
+    documents = document_store.get_all_documents(filters={"f1": ["1"]})
+    assert documents[0].text == "Doc1"
+    assert len(documents) == 1
+    assert {d.meta["vector_id"] for d in documents} == {"0"}
+
+
 def test_get_all_documents_with_correct_filters(document_store_with_docs):
     documents = document_store_with_docs.get_all_documents(filters={"meta_field": ["test2"]})
     assert len(documents) == 1
@@ -234,12 +256,29 @@ def test_multilabel_no_answer(document_store):
     document_store.delete_all_documents(index="haystack_test_multilabel_no_answer")
 
 
-@pytest.mark.parametrize("document_store_with_docs", ["elasticsearch"], indirect=True)
-def test_elasticsearch_update_meta(document_store_with_docs):
-    document = document_store_with_docs.query(query=None, filters={"name": ["filename1"]})[0]
-    document_store_with_docs.update_document_meta(document.id, meta={"meta_field": "updated_meta"})
-    updated_document = document_store_with_docs.query(query=None, filters={"name": ["filename1"]})[0]
-    assert updated_document.meta["meta_field"] == "updated_meta"
+@pytest.mark.parametrize("document_store", ["elasticsearch", "sql"], indirect=True)
+def test_elasticsearch_update_meta(document_store):
+    documents = [
+        Document(
+            text="Doc1",
+            meta={"vector_id": "1", "meta_key": "1"}
+        ),
+        Document(
+            text="Doc2",
+            meta={"vector_id": "2", "meta_key": "2"}
+        ),
+        Document(
+            text="Doc3",
+            meta={"vector_id": "3", "meta_key": "3"}
+        )
+    ]
+    document_store.write_documents(documents)
+    document_2 = document_store.get_all_documents(filters={"meta_key": ["2"]})[0]
+    document_store.update_document_meta(document_2.id, meta={"vector_id": "99", "meta_key": "2"})
+    updated_document = document_store.get_document_by_id(document_2.id)
+    assert len(updated_document.meta.keys()) == 2
+    assert updated_document.meta["vector_id"] == "99"
+    assert updated_document.meta["meta_key"] == "2"
 
 
 def test_elasticsearch_custom_fields(elasticsearch_fixture):