diff --git a/src/de/pangaea/metadataportal/processor/DocumentProcessor.java b/src/de/pangaea/metadataportal/processor/DocumentProcessor.java
index df48ced..7a2a78c 100644
--- a/src/de/pangaea/metadataportal/processor/DocumentProcessor.java
+++ b/src/de/pangaea/metadataportal/processor/DocumentProcessor.java
@@ -34,15 +34,21 @@
 import org.apache.commons.logging.LogFactory;
 import org.elasticsearch.ElasticsearchException;
 import org.elasticsearch.action.DocWriteRequest;
+import org.elasticsearch.action.DocWriteResponse.Result;
+import org.elasticsearch.action.bulk.BulkItemResponse;
 import org.elasticsearch.action.bulk.BulkProcessor;
 import org.elasticsearch.action.bulk.BulkRequest;
+import org.elasticsearch.action.bulk.BulkRequestBuilder;
 import org.elasticsearch.action.bulk.BulkResponse;
 import org.elasticsearch.action.delete.DeleteRequest;
+import org.elasticsearch.action.delete.DeleteResponse;
 import org.elasticsearch.action.get.GetResponse;
 import org.elasticsearch.action.index.IndexRequest;
+import org.elasticsearch.action.search.SearchResponse;
 import org.elasticsearch.client.Client;
 import org.elasticsearch.common.unit.ByteSizeUnit;
 import org.elasticsearch.common.unit.ByteSizeValue;
+import org.elasticsearch.common.unit.TimeValue;
 import org.elasticsearch.common.xcontent.XContentBuilder;
 import org.elasticsearch.common.xcontent.XContentFactory;
 import org.elasticsearch.common.xcontent.XContentType;
@@ -51,6 +57,9 @@
 import org.elasticsearch.index.query.QueryBuilders;
 import org.elasticsearch.index.reindex.BulkByScrollResponse;
 import org.elasticsearch.index.reindex.DeleteByQueryAction;
+import org.elasticsearch.search.SearchHit;
+import org.elasticsearch.search.sort.FieldSortBuilder;
+import org.elasticsearch.search.sort.SortBuilders;
 
 import de.pangaea.metadataportal.config.HarvesterConfig;
 import de.pangaea.metadataportal.utils.KeyValuePairs;
@@ -92,7 +101,7 @@ public final class DocumentProcessor {
   public static final int DEFAULT_MAX_QUEUE = 100;
   public static final int DEFAULT_CONCURRENT_BULK_REQUESTS = 1;
   public static final int DEFAULT_NUM_THREADS = 1;
-  public static final int DEFAULT_DELETE_UNSEEN_BULK_SIZE = 1000;
+  public static final int DEFAULT_DELETE_UNSEEN_BULK_SIZE = 10_000;
   public static final XContentType DEFAULT_CONTENT_TYPE = XContentType.CBOR;
 
   DocumentProcessor(Client client, HarvesterConfig iconfig, String targetIndex) {
@@ -211,19 +220,55 @@ public void addDocument(MetadataDocument mdoc) throws BackgroundFailure {
    */
   private void deleteUnseenDocuments(Set<String> validIdentifiers) {
     log.info("Removing metadata items not seen while harvesting...");
-    
-    final IdsQueryBuilder bld = QueryBuilders.idsQuery(iconfig.root.typeName);
-    bld.ids().addAll(validIdentifiers);
-    final QueryBuilder query = QueryBuilders.boolQuery()
-      .filter(QueryBuilders.termQuery(iconfig.root.fieldnameSource, iconfig.id))
-      .mustNot(bld);
-    
-    final BulkByScrollResponse response = DeleteByQueryAction.INSTANCE.newRequestBuilder(client)
-      .filter(query)
-      .source(targetIndex)
-      .get();
+    long deleted = 0L;
 
-    log.info("Deleted a total number of " + response.getDeleted() + " metadata items.");
+    if (validIdentifiers.size() < DEFAULT_DELETE_UNSEEN_BULK_SIZE) {
+      final IdsQueryBuilder bld = QueryBuilders.idsQuery(iconfig.root.typeName);
+      bld.ids().addAll(validIdentifiers);
+      final QueryBuilder query = QueryBuilders.boolQuery()
+        .filter(QueryBuilders.termQuery(iconfig.root.fieldnameSource, iconfig.id))
+        .mustNot(bld);
+      
+      final BulkByScrollResponse response = DeleteByQueryAction.INSTANCE.newRequestBuilder(client)
+        .filter(query)
+        .source(targetIndex)
+        .get();
+      deleted += response.getDeleted();
+    } else {
+      final TimeValue time = TimeValue.timeValueMinutes(10);
+      SearchResponse scrollResp = client.prepareSearch(targetIndex)
+        .setTypes(iconfig.root.typeName)
+        .setQuery(QueryBuilders.termQuery(iconfig.root.fieldnameSource, iconfig.id))
+        .setFetchSource(false)
+        .setSize(DEFAULT_DELETE_UNSEEN_BULK_SIZE)
+        .addSort(SortBuilders.fieldSort(FieldSortBuilder.DOC_FIELD_NAME))
+        .setScroll(time)
+        .get();
+      do {
+        final BulkRequestBuilder bulk = client.prepareBulk();
+        for (final SearchHit hit : scrollResp.getHits()) {
+          final String id = hit.getId();
+          if (!validIdentifiers.contains(id)) {
+            bulk.add(new DeleteRequest(targetIndex, iconfig.root.typeName, id));
+          }
+        }
+        if (bulk.numberOfActions() > 0) {
+          final BulkResponse bulkResp = bulk.get();
+          for (BulkItemResponse resp : bulkResp) {
+            final DeleteResponse delResp = resp.<DeleteResponse>getResponse();
+            if (delResp.getResult() != Result.DELETED) {
+              log.warn("Metadata item with ID '" + delResp.getId() + "' was not found when we tried to delete it.");
+            } else {
+              deleted++;
+            }
+          }
+        }
+        if (scrollResp.getScrollId() == null) break;
+        scrollResp = client.prepareSearchScroll(scrollResp.getScrollId()).setScroll(time).get();
+      } while (scrollResp.getHits().getHits().length > 0);      
+    }
+    
+    log.info("Deleted a total number of " + deleted + " metadata items.");
   }
   
   private Runnable getRunnable(final MetadataDocument mdoc) {