diff --git a/packages/strapi-generate-api/templates/mongoose/service.template b/packages/strapi-generate-api/templates/mongoose/service.template
index f9d4bcb4cf..62bb9045e3 100644
--- a/packages/strapi-generate-api/templates/mongoose/service.template
+++ b/packages/strapi-generate-api/templates/mongoose/service.template
@@ -30,12 +30,7 @@ module.exports = {
     const matchStage = hook.load().generateMatchStage(<%= globalID %>, filters); // Nested relation filter
     const aggregateStages = mergeStages(populateStage, matchStage);
 
-    const result = <%= globalID %>.aggregate([
-      {
-        $match: filters.where, // Direct relation filter
-      },
-      ...aggregateStages
-    ])
+    const result = <%= globalID %>.aggregate(aggregateStages)
       .skip(filters.start)
       .limit(filters.limit);
 
diff --git a/packages/strapi-plugin-users-permissions/config/queries/mongoose.js b/packages/strapi-plugin-users-permissions/config/queries/mongoose.js
index 35a7adc2aa..88e988ed95 100644
--- a/packages/strapi-plugin-users-permissions/config/queries/mongoose.js
+++ b/packages/strapi-plugin-users-permissions/config/queries/mongoose.js
@@ -10,12 +10,7 @@ module.exports = {
     const matchStage = hook.load().generateMatchStage(this, filters); // Nested relation filter
     const aggregateStages = mergeStages(populateStage, matchStage);
 
-    const result = this.aggregate([
-      {
-        $match: filters.where || {}, // Direct relation filter
-      },
-      ...aggregateStages
-    ]);
+    const result = this.aggregate(aggregateStages);
 
     if (_.has(filters, 'start')) result.skip(filters.start);
     if (_.has(filters, 'limit')) result.limit(filters.limit);
diff --git a/packages/strapi-utils/lib/models.js b/packages/strapi-utils/lib/models.js
index 5766febb69..ec80dc1658 100644
--- a/packages/strapi-utils/lib/models.js
+++ b/packages/strapi-utils/lib/models.js
@@ -364,7 +364,7 @@ module.exports = {
           filter: details.filter,
         };
 
-        if (infos.nature === 'manyToMany' && !association.plugin && definition.orm === 'bookshelf') {
+        if (infos.nature === 'manyToMany' && definition.orm === 'bookshelf') {
           ast.tableCollectionName = this.getCollectionName(association, details);
         }
 
@@ -453,6 +453,7 @@ module.exports = {
       this.processValues({ model, models, convertor, postProcessValue }),
       this.processPredicates({ model, models, convertor }),
       this.processGeneratedResults(),
+      this.mergeWhereAndRelationPayloads()
     ])(_filter);
   },
 
@@ -680,5 +681,17 @@ module.exports = {
         return updatedFilter;
       });
     };
+  },
+
+  mergeWhereAndRelationPayloads: function() {
+    return filter => {
+      return {
+        ...filter, // Normally here we need to omit where key
+        relations: {
+          ...filter.where,
+          relations: filter.relations
+        }
+      };
+    };
   }
 };