diff --git a/packages/core/src/hydration/ObjectHydrator.ts b/packages/core/src/hydration/ObjectHydrator.ts
index 1b1f76387479..d1149eb6db32 100644
--- a/packages/core/src/hydration/ObjectHydrator.ts
+++ b/packages/core/src/hydration/ObjectHydrator.ts
@@ -96,14 +96,7 @@ export class ObjectHydrator extends Hydrator {
           `  if (${preCond}typeof data${dataKey} !== 'undefined') {`,
           `    if (convertCustomTypes) {`,
           `      const value = convertToJSValue_${convertorKey}(data${dataKey});`,
-        );
-
-        // make sure the value is comparable, but skip this for JSON props as it can result in double encoding
-        if (!(prop.customType instanceof JsonType)) {
-          ret.push(`      data${dataKey} = convertToDatabaseValue_${convertorKey}(value);`);
-        }
-
-        ret.push(
+          `      data${dataKey} = convertToDatabaseValue_${convertorKey}(value);`, // make sure the value is comparable
           `      entity${entityKey} = value;`,
           `    } else {`,
           `      entity${entityKey} = data${dataKey};`,
diff --git a/tests/issues/GH4078.test.ts b/tests/issues/GH4078.test.ts
new file mode 100644
index 000000000000..7d3b61b33e16
--- /dev/null
+++ b/tests/issues/GH4078.test.ts
@@ -0,0 +1,54 @@
+import { Entity, JsonType, PrimaryKey, Property } from '@mikro-orm/core';
+import { MikroORM } from '@mikro-orm/mysql';
+import { mockLogger } from '../helpers';
+
+type Setup = {
+  limits?: boolean;
+  fallbackFees?: boolean;
+};
+
+@Entity()
+class Contract {
+
+  @PrimaryKey()
+  id!: number;
+
+  @Property()
+  title!: string;
+
+  @Property({ type: JsonType, nullable: true })
+  setup: Setup | null = null;
+
+}
+
+let orm: MikroORM;
+
+beforeAll(async () => {
+  orm = await MikroORM.init({
+    entities: [Contract],
+    dbName: `mikro_orm_test_4078`,
+    port: 3308,
+  });
+
+  await orm.schema.refreshDatabase();
+});
+
+afterAll(async () => {
+  await orm.close(true);
+});
+
+test('4078', async () => {
+  await orm.em.insert(Contract, {
+    id: 1,
+    title: 't',
+    setup: {
+      limits: true,
+      fallbackFees: false,
+    },
+  });
+  orm.em.clear();
+  await orm.em.findOneOrFail(Contract, 1);
+  const mock = mockLogger(orm);
+  await orm.em.flush();
+  expect(mock).not.toBeCalled();
+});