diff --git a/packages/knex/src/query/QueryBuilder.ts b/packages/knex/src/query/QueryBuilder.ts
index 9cf11d250c87..0258a5387260 100644
--- a/packages/knex/src/query/QueryBuilder.ts
+++ b/packages/knex/src/query/QueryBuilder.ts
@@ -482,7 +482,7 @@ export class QueryBuilder<T extends AnyEntity<T> = AnyEntity> {
   }
 
   getKnex(): KnexQueryBuilder {
-    const tableName = this.helper.getTableName(this.entityName) + (this.finalized && [QueryType.SELECT, QueryType.COUNT].includes(this.type) ? ` as ${this.alias}` : '');
+    const tableName = this.helper.getTableName(this.entityName) + (this.finalized && this.helper.isTableNameAliasRequired(this.type) ? ` as ${this.alias}` : '');
     const qb = this.knex(tableName);
 
     if (this.context) {
@@ -575,7 +575,7 @@ export class QueryBuilder<T extends AnyEntity<T> = AnyEntity> {
     this.type = type;
     this._aliasMap[this.alias] = this.entityName;
 
-    if (![QueryType.SELECT, QueryType.COUNT].includes(type)) {
+    if (!this.helper.isTableNameAliasRequired(type)) {
       delete this._fields;
     }
 
diff --git a/packages/knex/src/query/QueryBuilderHelper.ts b/packages/knex/src/query/QueryBuilderHelper.ts
index 199ae49dbd56..080466e63ac9 100644
--- a/packages/knex/src/query/QueryBuilderHelper.ts
+++ b/packages/knex/src/query/QueryBuilderHelper.ts
@@ -30,6 +30,7 @@ export class QueryBuilderHelper {
   mapper(field: string, type?: QueryType): string;
   mapper(field: string, type?: QueryType, value?: any, alias?: string | null): string;
   mapper(field: string, type = QueryType.SELECT, value?: any, alias?: string | null): string | Raw {
+    const isTableNameAliasRequired = this.isTableNameAliasRequired(type);
     const fields = Utils.splitPrimaryKeys(field);
 
     if (fields.length > 1) {
@@ -43,11 +44,11 @@ export class QueryBuilderHelper {
     const noPrefix = prop && prop.persist === false;
 
     if (prop?.fieldNameRaw) {
-      return this.knex.raw(this.prefix(field, true));
+      return this.knex.raw(this.prefix(field, isTableNameAliasRequired));
     }
 
     if (prop?.customType?.convertToJSValueSQL) {
-      const prefixed = this.prefix(field, true, true);
+      const prefixed = this.prefix(field, isTableNameAliasRequired, true);
       const valueSQL = prop.customType.convertToJSValueSQL!(prefixed, this.platform);
 
       if (alias === null) {
@@ -71,7 +72,7 @@ export class QueryBuilderHelper {
       return this.knex.raw(ret, value);
     }
 
-    if (![QueryType.SELECT, QueryType.COUNT].includes(type) || this.isPrefixed(ret) || noPrefix) {
+    if (!isTableNameAliasRequired || this.isPrefixed(ret) || noPrefix) {
       return ret;
     }
 
@@ -580,4 +581,8 @@ export class QueryBuilderHelper {
     return meta ? meta.properties[field] : undefined;
   }
 
+  isTableNameAliasRequired(type: QueryType): boolean {
+    return [QueryType.SELECT, QueryType.COUNT].includes(type);
+  }
+
 }
diff --git a/tests/features/embeddables/embedded-entities.postgres.test.ts b/tests/features/embeddables/embedded-entities.postgres.test.ts
index b957db674fbb..66afbf1acec6 100644
--- a/tests/features/embeddables/embedded-entities.postgres.test.ts
+++ b/tests/features/embeddables/embedded-entities.postgres.test.ts
@@ -260,6 +260,33 @@ describe('embedded entities in postgresql', () => {
     });
   });
 
+
+  test('native update entity', async () => {
+    const user = new User();
+    wrap(user).assign({
+      address1: { street: 'Downing street 10', number: 3, postalCode: '123', city: 'London 1', country: 'UK 1' },
+      address2: { street: 'Downing street 11', number: 3, city: 'London 2', country: 'UK 2' },
+      address3: { street: 'Downing street 12', number: 3, postalCode: '789', city: 'London 3', country: 'UK 3' },
+      address4: { street: 'Downing street 10', number: 3, postalCode: '123', city: 'London 1', country: 'UK 1' },
+    }, { em: orm.em });
+
+    await orm.em.persistAndFlush(user);
+
+    await orm.em.nativeUpdate(User, {
+      address4: {
+        number: {
+          $gt: 2,
+        },
+      },
+    }, {
+      after: 2,
+    });
+    orm.em.clear();
+
+    const userAfterUpdate = await orm.em.findOne(User, user.id);
+    expect(userAfterUpdate?.after).toBe(2);
+  });
+
   test('query by complex custom expressions with JSON operator and casting (GH issue 1261)', async () => {
     const user = new User();
     user.address1 = new Address1('Test', 10, '12000', 'Prague', 'CZ');