diff --git a/packages/strapi-hook-bookshelf/lib/query-utils.js b/packages/strapi-hook-bookshelf/lib/query-utils.js
index 16ea8018ec..25d5d41b06 100644
--- a/packages/strapi-hook-bookshelf/lib/query-utils.js
+++ b/packages/strapi-hook-bookshelf/lib/query-utils.js
@@ -14,9 +14,23 @@ class QueryBuilder {
         let fieldKey = `${model.collectionName}.${attributeKey}`;
         if (association) {
           if (association.nature === 'manyToMany') {
-            const { attribute, column } = model.attributes[key];
+            const { attribute, column } = model.attributes[association.via];
             fieldKey = `${association.tableCollectionName}.${attribute}_${column}`;
           }
+
+          /**
+           * If for instance we want to filter on the model relation, such as
+           * {
+           *   product: {
+           *     method: 'whereIn',
+           *     value: ["1", "2", "3"]
+           *   }
+           * }
+           * the fieldKey should be "products.id" and not "products.product"
+           */
+          if (attributeKey === key) {
+            fieldKey = `${model.collectionName}.${model.primaryKey}`;
+          }
         }
 
         if (value.symbol) {
@@ -108,7 +122,7 @@ class QueryBuilder {
 
         qb.innerJoin(
           relationTable,
-          `${association.tableCollectionName}.${strapiModel.attributes[key].attribute}_${strapiModel.attributes[key].column}`,
+          `${association.tableCollectionName}.${strapiModel.attributes[association.alias].attribute}_${strapiModel.attributes[association.alias].column}`,
           `${relationTable}.${astModel.primaryKey}`,
         );
       } else {
diff --git a/packages/strapi-plugin-graphql/services/Loaders.js b/packages/strapi-plugin-graphql/services/Loaders.js
index 6c7376c5d4..787319bef7 100644
--- a/packages/strapi-plugin-graphql/services/Loaders.js
+++ b/packages/strapi-plugin-graphql/services/Loaders.js
@@ -97,7 +97,26 @@ module.exports = {
 
         return data
           .filter(entry => {
-            const entryValue = entry[ids.alias][astModel.primaryKey];
+            /**
+             * In some cases (Mongoose for instance) the entry will be populated so we need to access its value using the primary key
+             * Example
+             * // Mongoose
+             * entry = {
+             *   product: {
+             *     _id: "some_id", // the value is entry["product"]["_id"]
+             *     price: 10
+             *   },
+             *   company: "strapi"
+             * }
+             * // Bookshelf
+             * entry = {
+             *  product: 1, // the value is entry["product"]
+             *  company: "strapi"
+             * }
+             */
+            const entryValue = _.isUndefined(entry[ids.alias][astModel.primaryKey])
+              ? entry[ids.alias]
+              : entry[ids.alias][astModel.primaryKey];
             return entryValue.toString() === ids.value.toString();
           })
           .slice(skip, skip + limit);