diff --git a/registry-persistence/src/main/java/org/gbif/registry/persistence/mapper/collections/CollectionMapper.java b/registry-persistence/src/main/java/org/gbif/registry/persistence/mapper/collections/CollectionMapper.java
index de2826d86..a2ce5f2e5 100644
--- a/registry-persistence/src/main/java/org/gbif/registry/persistence/mapper/collections/CollectionMapper.java
+++ b/registry-persistence/src/main/java/org/gbif/registry/persistence/mapper/collections/CollectionMapper.java
@@ -63,4 +63,6 @@ public interface CollectionMapper
    */
   List<MasterSourceOrganizationDto> findByDatasetOrganizationAsMasterSource(
       @Param("organizationKey") UUID organizationKey);
+
+  List<UUID> getAllKeys();
 }
diff --git a/registry-persistence/src/main/java/org/gbif/registry/persistence/mapper/collections/InstitutionMapper.java b/registry-persistence/src/main/java/org/gbif/registry/persistence/mapper/collections/InstitutionMapper.java
index 400e1f4b6..82360c45d 100644
--- a/registry-persistence/src/main/java/org/gbif/registry/persistence/mapper/collections/InstitutionMapper.java
+++ b/registry-persistence/src/main/java/org/gbif/registry/persistence/mapper/collections/InstitutionMapper.java
@@ -50,4 +50,6 @@ void convertToCollection(
       @Param("institutionKey") UUID institutionKey, @Param("collectionKey") UUID collectionKey);
 
   List<InstitutionGeoJsonDto> listGeoJson(@Param("params") InstitutionSearchParams searchParams);
+
+  List<UUID> getAllKeys();
 }
diff --git a/registry-persistence/src/main/resources/org/gbif/registry/persistence/mapper/collections/CollectionMapper.xml b/registry-persistence/src/main/resources/org/gbif/registry/persistence/mapper/collections/CollectionMapper.xml
index 47ed5b239..1d9964d74 100644
--- a/registry-persistence/src/main/resources/org/gbif/registry/persistence/mapper/collections/CollectionMapper.xml
+++ b/registry-persistence/src/main/resources/org/gbif/registry/persistence/mapper/collections/CollectionMapper.xml
@@ -426,6 +426,10 @@
     WHERE key = aux.entity_key::uuid
   </update>
 
+  <select id="getAllKeys" resultType="java.util.UUID">
+    SELECT key FROM collection WHERE deleted IS NULL
+  </select>
+
   <!-- new model contacts -->
   <select id="listContactPersons" resultMap="org.gbif.registry.persistence.mapper.collections.CollectionContactMapper.CONTACT_MAP">
     SELECT <include refid="org.gbif.registry.persistence.mapper.collections.CollectionContactMapper.CONTACT_READ_FIELDS"/>
diff --git a/registry-persistence/src/main/resources/org/gbif/registry/persistence/mapper/collections/InstitutionMapper.xml b/registry-persistence/src/main/resources/org/gbif/registry/persistence/mapper/collections/InstitutionMapper.xml
index 63514dff5..479ed786e 100644
--- a/registry-persistence/src/main/resources/org/gbif/registry/persistence/mapper/collections/InstitutionMapper.xml
+++ b/registry-persistence/src/main/resources/org/gbif/registry/persistence/mapper/collections/InstitutionMapper.xml
@@ -437,6 +437,10 @@
     WHERE key = aux.entity_key::uuid
   </update>
 
+  <select id="getAllKeys" resultType="java.util.UUID">
+    SELECT key FROM institution WHERE deleted IS NULL
+  </select>
+
   <!-- LOOKUP -->
   <sql id="LOOKUP_MATCH_FIELDS">
     i.key, i.name, i.code, i.address_key, i.mailing_address_key, akeys(i.alternative_codes) AS alternative_codes, i.active
diff --git a/registry-ws/src/main/java/org/gbif/registry/ws/resources/scheduled/GRSciCollCountsUpdaterService.java b/registry-ws/src/main/java/org/gbif/registry/ws/resources/scheduled/GRSciCollCountsUpdaterService.java
index 22ea37d49..6baf5f31a 100644
--- a/registry-ws/src/main/java/org/gbif/registry/ws/resources/scheduled/GRSciCollCountsUpdaterService.java
+++ b/registry-ws/src/main/java/org/gbif/registry/ws/resources/scheduled/GRSciCollCountsUpdaterService.java
@@ -28,11 +28,9 @@
 import org.gbif.ws.client.ClientBuilder;
 import org.gbif.ws.json.JacksonJsonObjectMapperProvider;
 
-import java.util.Arrays;
-import java.util.HashMap;
-import java.util.Map;
-import java.util.UUID;
+import java.util.*;
 import java.util.function.Function;
+import java.util.stream.Collectors;
 
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.beans.factory.annotation.Value;
@@ -81,9 +79,9 @@ public void scheduleUpdateCounts() {
   private void updateCounts() {
     log.info("Updating GRSciColl counts");
 
-    long institutionsCount = institutionMapper.count(InstitutionSearchParams.builder().build());
-    long collectionsCount = collectionMapper.count(CollectionSearchParams.builder().build());
-    long facetCount = Math.max(institutionsCount, collectionsCount);
+    List<UUID> institutionKeys = institutionMapper.getAllKeys();
+    List<UUID> collectionKeys = collectionMapper.getAllKeys();
+    long facetCount = Math.max(institutionKeys.size(), collectionKeys.size());
 
     OccurrenceSearchRequest request = new OccurrenceSearchRequest();
     request.setLimit(0);
@@ -93,8 +91,32 @@ private void updateCounts() {
     SearchResponse<Occurrence, OccurrenceSearchParameter> occurrenceCountsResponse =
         occurrenceWsSearchClient.search(request);
 
-    Map<UUID, Count> institutionsCounts = new HashMap<>();
-    Map<UUID, Count> collectionsCounts = new HashMap<>();
+    // all entities are initialised to zero because the occurrence response doesn't return values
+    // with count zero and if they used to have records we need to update them to zero
+    Map<UUID, Count> institutionsCounts =
+        institutionKeys.stream()
+            .collect(
+                Collectors.toMap(
+                    k -> k,
+                    k -> {
+                      Count c = new Count();
+                      c.setKey(k);
+                      c.setOccurrenceCount(0);
+                      c.setTypeSpecimenCount(0);
+                      return c;
+                    }));
+    Map<UUID, Count> collectionsCounts =
+        collectionKeys.stream()
+            .collect(
+                Collectors.toMap(
+                    k -> k,
+                    k -> {
+                      Count c = new Count();
+                      c.setKey(k);
+                      c.setOccurrenceCount(0);
+                      c.setTypeSpecimenCount(0);
+                      return c;
+                    }));
 
     Function<OccurrenceSearchParameter, Map<UUID, Count>> mapCountsSupplier =
         p -> {