diff --git a/modules/percolator/src/main/java/org/elasticsearch/percolator/PercolatorMatchedSlotSubFetchPhase.java b/modules/percolator/src/main/java/org/elasticsearch/percolator/PercolatorMatchedSlotSubFetchPhase.java
index 5548cc90e1f..40f6f9a40ff 100644
--- a/modules/percolator/src/main/java/org/elasticsearch/percolator/PercolatorMatchedSlotSubFetchPhase.java
+++ b/modules/percolator/src/main/java/org/elasticsearch/percolator/PercolatorMatchedSlotSubFetchPhase.java
@@ -20,6 +20,8 @@ package org.elasticsearch.percolator;
 
 import org.apache.lucene.index.LeafReaderContext;
 import org.apache.lucene.index.ReaderUtil;
+import org.apache.lucene.search.BooleanClause;
+import org.apache.lucene.search.BooleanQuery;
 import org.apache.lucene.search.IndexSearcher;
 import org.apache.lucene.search.Query;
 import org.apache.lucene.search.ScoreMode;
@@ -69,12 +71,8 @@ final class PercolatorMatchedSlotSubFetchPhase implements FetchSubPhase {
         for (PercolateQuery percolateQuery : percolateQueries) {
             String fieldName = singlePercolateQuery ? FIELD_NAME_PREFIX : FIELD_NAME_PREFIX + "_" + percolateQuery.getName();
             IndexSearcher percolatorIndexSearcher = percolateQuery.getPercolatorIndexSearcher();
-            // there is a bug in lucene's MemoryIndex that doesn't allow us to use docValues here...
-            // See https://issues.apache.org/jira/browse/LUCENE-8055
-            // for now we just use version 6.0 version to find nested parent
-            final Version version = Version.V_6_0_0; //context.mapperService().getIndexSettings().getIndexVersionCreated();
-            Weight weight = percolatorIndexSearcher.createWeight(percolatorIndexSearcher.rewrite(Queries.newNonNestedFilter(version)),
-                    ScoreMode.COMPLETE_NO_SCORES, 1f);
+            Query nonNestedFilter = percolatorIndexSearcher.rewrite(Queries.newNonNestedFilter(Version.CURRENT));
+            Weight weight = percolatorIndexSearcher.createWeight(nonNestedFilter, ScoreMode.COMPLETE_NO_SCORES, 1f);
             Scorer s = weight.scorer(percolatorIndexSearcher.getIndexReader().leaves().get(0));
             int memoryIndexMaxDoc = percolatorIndexSearcher.getIndexReader().maxDoc();
             BitSet rootDocs = BitSet.of(s.iterator(), memoryIndexMaxDoc);
@@ -94,6 +92,13 @@ final class PercolatorMatchedSlotSubFetchPhase implements FetchSubPhase {
                     // This is not a document with a percolator field.
                     continue;
                 }
+                if (hasNestedDocs) {
+                    // Ensures that we filter out nested documents
+                    query = new BooleanQuery.Builder()
+                        .add(query, BooleanClause.Occur.MUST)
+                        .add(nonNestedFilter, BooleanClause.Occur.FILTER)
+                        .build();
+                }
 
                 TopDocs topDocs = percolatorIndexSearcher.search(query, memoryIndexMaxDoc, new Sort(SortField.FIELD_DOC));
                 if (topDocs.totalHits.value == 0) {
diff --git a/modules/percolator/src/test/java/org/elasticsearch/percolator/PercolatorQuerySearchIT.java b/modules/percolator/src/test/java/org/elasticsearch/percolator/PercolatorQuerySearchIT.java
index 3e7d5611ec4..e4d0f3b1148 100644
--- a/modules/percolator/src/test/java/org/elasticsearch/percolator/PercolatorQuerySearchIT.java
+++ b/modules/percolator/src/test/java/org/elasticsearch/percolator/PercolatorQuerySearchIT.java
@@ -751,6 +751,7 @@ public class PercolatorQuerySearchIT extends ESIntegTestCase {
     public void testPercolateQueryWithNestedDocuments() throws Exception {
         XContentBuilder mapping = XContentFactory.jsonBuilder();
         mapping.startObject().startObject("properties").startObject("query").field("type", "percolator").endObject()
+                .startObject("id").field("type", "keyword").endObject()
                 .startObject("companyname").field("type", "text").endObject().startObject("employee").field("type", "nested")
                 .startObject("properties").startObject("name").field("type", "text").endObject().endObject().endObject().endObject()
                 .endObject();
@@ -758,16 +759,24 @@ public class PercolatorQuerySearchIT extends ESIntegTestCase {
                 .addMapping("employee", mapping)
         );
         client().prepareIndex("test", "employee", "q1").setSource(jsonBuilder().startObject()
+                .field("id", "q1")
                 .field("query", QueryBuilders.nestedQuery("employee",
                         QueryBuilders.matchQuery("employee.name", "virginia potts").operator(Operator.AND), ScoreMode.Avg)
                 ).endObject())
                 .get();
         // this query should never match as it doesn't use nested query:
         client().prepareIndex("test", "employee", "q2").setSource(jsonBuilder().startObject()
+                .field("id", "q2")
                 .field("query", QueryBuilders.matchQuery("employee.name", "virginia")).endObject())
                 .get();
         client().admin().indices().prepareRefresh().get();
 
+        client().prepareIndex("test", "employee", "q3").setSource(jsonBuilder().startObject()
+            .field("id", "q3")
+            .field("query", QueryBuilders.matchAllQuery()).endObject())
+            .get();
+        client().admin().indices().prepareRefresh().get();
+
         SearchResponse response = client().prepareSearch()
                 .setQuery(new PercolateQueryBuilder("query",
                         BytesReference.bytes(XContentFactory.jsonBuilder()
@@ -777,10 +786,11 @@ public class PercolatorQuerySearchIT extends ESIntegTestCase {
                                     .startObject().field("name", "tony stark").endObject()
                                 .endArray()
                             .endObject()), XContentType.JSON))
-                .addSort("_doc", SortOrder.ASC)
+                .addSort("id", SortOrder.ASC)
                 .get();
-        assertHitCount(response, 1);
+        assertHitCount(response, 2);
         assertThat(response.getHits().getAt(0).getId(), equalTo("q1"));
+        assertThat(response.getHits().getAt(1).getId(), equalTo("q3"));
 
         response = client().prepareSearch()
                 .setQuery(new PercolateQueryBuilder("query",
@@ -791,17 +801,19 @@ public class PercolatorQuerySearchIT extends ESIntegTestCase {
                                     .startObject().field("name", "tony stark").endObject()
                                 .endArray()
                             .endObject()), XContentType.JSON))
-                .addSort("_doc", SortOrder.ASC)
+                .addSort("id", SortOrder.ASC)
                 .get();
-        assertHitCount(response, 0);
+        assertHitCount(response, 1);
+        assertThat(response.getHits().getAt(0).getId(), equalTo("q3"));
 
         response = client().prepareSearch()
                 .setQuery(new PercolateQueryBuilder("query",
                         BytesReference.bytes(XContentFactory.jsonBuilder().startObject().field("companyname", "notstark").endObject()),
                     XContentType.JSON))
-                .addSort("_doc", SortOrder.ASC)
+                .addSort("id", SortOrder.ASC)
                 .get();
-        assertHitCount(response, 0);
+        assertHitCount(response, 1);
+        assertThat(response.getHits().getAt(0).getId(), equalTo("q3"));
 
         response = client().prepareSearch()
             .setQuery(new PercolateQueryBuilder("query", Arrays.asList(
@@ -818,13 +830,21 @@ public class PercolatorQuerySearchIT extends ESIntegTestCase {
                     .startObject().field("name", "peter parker").endObject()
                     .startObject().field("name", "virginia potts").endObject()
                     .endArray()
+                    .endObject()),
+                BytesReference.bytes(XContentFactory.jsonBuilder()
+                    .startObject().field("companyname", "stark")
+                    .startArray("employee")
+                        .startObject().field("name", "peter parker").endObject()
+                    .endArray()
                     .endObject())
             ), XContentType.JSON))
-            .addSort("_doc", SortOrder.ASC)
+            .addSort("id", SortOrder.ASC)
             .get();
-        assertHitCount(response, 1);
+        assertHitCount(response, 2);
         assertThat(response.getHits().getAt(0).getId(), equalTo("q1"));
         assertThat(response.getHits().getAt(0).getFields().get("_percolator_document_slot").getValues(), equalTo(Arrays.asList(0, 1)));
+        assertThat(response.getHits().getAt(1).getId(), equalTo("q3"));
+        assertThat(response.getHits().getAt(1).getFields().get("_percolator_document_slot").getValues(), equalTo(Arrays.asList(0, 1, 2)));
     }
 
     public void testPercolatorQueryViaMultiSearch() throws Exception {