diff --git a/spring-data-mongodb/src/main/java/org/springframework/data/mongodb/core/convert/QueryMapper.java b/spring-data-mongodb/src/main/java/org/springframework/data/mongodb/core/convert/QueryMapper.java
index 51c9e50c0..a49cc2db7 100644
--- a/spring-data-mongodb/src/main/java/org/springframework/data/mongodb/core/convert/QueryMapper.java
+++ b/spring-data-mongodb/src/main/java/org/springframework/data/mongodb/core/convert/QueryMapper.java
@@ -696,7 +696,8 @@ public class QueryMapper {
 	@Nullable
 	private Object applyFieldTargetTypeHintToValue(Field documentField, @Nullable Object value) {
 
-		if (value == null || documentField.getProperty() == null || !documentField.getProperty().hasExplicitWriteTarget()) {
+		if (value == null || documentField.getProperty() == null || !documentField.getProperty().hasExplicitWriteTarget()
+				|| value instanceof Document || value instanceof DBObject) {
 			return value;
 		}
 
diff --git a/spring-data-mongodb/src/test/java/org/springframework/data/mongodb/core/convert/QueryMapperUnitTests.java b/spring-data-mongodb/src/test/java/org/springframework/data/mongodb/core/convert/QueryMapperUnitTests.java
index c6dccb829..60d6e47dd 100755
--- a/spring-data-mongodb/src/test/java/org/springframework/data/mongodb/core/convert/QueryMapperUnitTests.java
+++ b/spring-data-mongodb/src/test/java/org/springframework/data/mongodb/core/convert/QueryMapperUnitTests.java
@@ -33,11 +33,6 @@ import org.bson.types.Code;
 import org.bson.types.ObjectId;
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
-import org.junit.jupiter.api.extension.ExtendWith;
-import org.mockito.Mock;
-import org.mockito.junit.jupiter.MockitoExtension;
-import org.mockito.junit.jupiter.MockitoSettings;
-import org.mockito.quality.Strictness;
 
 import org.springframework.core.convert.converter.Converter;
 import org.springframework.data.annotation.Id;
@@ -45,7 +40,6 @@ import org.springframework.data.convert.WritingConverter;
 import org.springframework.data.domain.Sort;
 import org.springframework.data.domain.Sort.Direction;
 import org.springframework.data.geo.Point;
-import org.springframework.data.mongodb.MongoDatabaseFactory;
 import org.springframework.data.mongodb.core.DocumentTestUtils;
 import org.springframework.data.mongodb.core.Person;
 import org.springframework.data.mongodb.core.geo.GeoJsonPoint;
@@ -55,6 +49,7 @@ import org.springframework.data.mongodb.core.mapping.DBRef;
 import org.springframework.data.mongodb.core.mapping.Document;
 import org.springframework.data.mongodb.core.mapping.Field;
 import org.springframework.data.mongodb.core.mapping.FieldType;
+import org.springframework.data.mongodb.core.mapping.MongoId;
 import org.springframework.data.mongodb.core.mapping.MongoMappingContext;
 import org.springframework.data.mongodb.core.mapping.MongoPersistentEntity;
 import org.springframework.data.mongodb.core.mapping.TextScore;
@@ -77,22 +72,21 @@ import com.mongodb.client.model.Filters;
  * @author Mark Paluch
  * @author David Julia
  */
-@ExtendWith(MockitoExtension.class)
-@MockitoSettings(strictness = Strictness.LENIENT)
 public class QueryMapperUnitTests {
 
 	private QueryMapper mapper;
 	private MongoMappingContext context;
 	private MappingMongoConverter converter;
 
-	@Mock MongoDatabaseFactory factory;
-
 	@BeforeEach
 	void beforeEach() {
 
+		MongoCustomConversions conversions = new MongoCustomConversions();
 		this.context = new MongoMappingContext();
+		this.context.setSimpleTypeHolder(conversions.getSimpleTypeHolder());
 
-		this.converter = new MappingMongoConverter(new DefaultDbRefResolver(factory), context);
+		this.converter = new MappingMongoConverter(NoOpDbRefResolver.INSTANCE, context);
+		this.converter.setCustomConversions(conversions);
 		this.converter.afterPropertiesSet();
 
 		this.mapper = new QueryMapper(converter);
@@ -1152,6 +1146,25 @@ public class QueryMapperUnitTests {
 				.isEqualTo(new org.bson.Document("address.street", "1007 Mountain Drive"));
 	}
 
+	@Test // GH-3783
+	void retainsId$InWithStringArray() {
+
+		org.bson.Document mappedQuery = mapper.getMappedObject(
+				org.bson.Document.parse("{ _id : { $in: [\"5b8bedceb1e0bfc07b008828\"]}}"),
+				context.getPersistentEntity(WithExplicitStringId.class));
+		assertThat(mappedQuery.get("_id")).isEqualTo(org.bson.Document.parse("{ $in: [\"5b8bedceb1e0bfc07b008828\"]}"));
+	}
+
+	@Test // GH-3783
+	void mapsId$InInToObjectIds() {
+
+		org.bson.Document mappedQuery = mapper.getMappedObject(
+				org.bson.Document.parse("{ _id : { $in: [\"5b8bedceb1e0bfc07b008828\"]}}"),
+				context.getPersistentEntity(ClassWithDefaultId.class));
+		assertThat(mappedQuery.get("_id"))
+				.isEqualTo(org.bson.Document.parse("{ $in: [ {$oid: \"5b8bedceb1e0bfc07b008828\" } ]}"));
+	}
+
 	class WithDeepArrayNesting {
 
 		List<WithNestedArray> level0;
@@ -1215,6 +1228,18 @@ public class QueryMapperUnitTests {
 		@Id private String foo;
 	}
 
+	class WithStringId {
+
+		@MongoId String id;
+		String name;
+	}
+
+	class WithExplicitStringId {
+
+		@MongoId(FieldType.STRING) String id;
+		String name;
+	}
+
 	class BigIntegerId {
 
 		@Id private BigInteger id;