diff --git a/harvesters/src/main/java/org/fao/geonet/kernel/harvest/harvester/simpleurl/Harvester.java b/harvesters/src/main/java/org/fao/geonet/kernel/harvest/harvester/simpleurl/Harvester.java
index 2cd1100dc6d..254fac91f84 100644
--- a/harvesters/src/main/java/org/fao/geonet/kernel/harvest/harvester/simpleurl/Harvester.java
+++ b/harvesters/src/main/java/org/fao/geonet/kernel/harvest/harvester/simpleurl/Harvester.java
@@ -105,6 +105,7 @@ public HarvestResult harvest(Logger log) throws Exception {
         String[] urlList = params.url.split("\n");
         boolean error = false;
         Aligner aligner = new Aligner(cancelMonitor, context, params, log);
+        Set<String> listOfUuids = new HashSet<>();
 
         for (String url : urlList) {
             log.debug("Loading URL: " + url);
@@ -151,7 +152,6 @@ public HarvestResult harvest(Logger log) throws Exception {
                         params.numberOfRecordPath, e.getMessage()));
                 }
             }
-            Map<String, Element> allUuids = new HashMap<>();
             try {
                 List<String> listOfUrlForPages = buildListOfUrl(params, numberOfRecordsToHarvest);
                 for (int i = 0; i < listOfUrlForPages.size(); i++) {
@@ -166,7 +166,6 @@ public HarvestResult harvest(Logger log) throws Exception {
                     if (StringUtils.isNotEmpty(params.loopElement)
                         || type == SimpleUrlResourceType.RDFXML) {
                         Map<String, Element> uuids = new HashMap<>();
-
                         try {
                             if (type == SimpleUrlResourceType.XML) {
                                 collectRecordsFromXml(xmlObj, uuids, aligner);
@@ -176,7 +175,7 @@ public HarvestResult harvest(Logger log) throws Exception {
                                 collectRecordsFromJson(jsonObj, uuids, aligner);
                             }
                             aligner.align(uuids, errors);
-                            allUuids.putAll(uuids);
+                            listOfUuids.addAll(uuids.keySet());
                         } catch (Exception e) {
                             errors.add(new HarvestError(this.context, e));
                             log.error(String.format("Failed to collect record in response at path %s. Error is: %s",
@@ -184,7 +183,6 @@ public HarvestResult harvest(Logger log) throws Exception {
                         }
                     }
                 }
-                aligner.cleanupRemovedRecords(allUuids.keySet());
             } catch (Exception t) {
                 error = true;
                 log.error("Unknown error trying to harvest");
@@ -198,11 +196,12 @@ public HarvestResult harvest(Logger log) throws Exception {
                 errors.add(new HarvestError(context, t));
             }
 
-            log.info("Total records processed in all searches :" + allUuids.size());
+            log.info("Total records processed in all searches :" + listOfUuids.size());
             if (error) {
                 log.warning("Due to previous errors the align process has not been called");
             }
         }
+        aligner.cleanupRemovedRecords(listOfUuids);
         return aligner.getResult();
     }