Just use the @Query annotation on that method.
public interface CustomRepository extends MongoRepository<PracticeQuestion, String> {
@Query(value = "{ 'userId' : ?0, 'questions.questionID' : ?1 }", fields = "{ 'questions.questionID' : 1 }")
List<PracticeQuestion> findByUserIdAndQuestionsQuestionID(int userId, int questionID);
}
By adding the fields part of the @Query annotation, you are telling Mongo to only return that part of the document. Beware though, it still returns the entire document in the same format – just missing everything you did not specify. So your code will still have to return List<PracticeQuestion> and you will have to do:
foreach (PracticeQuestion pq : practiceQuestions) {
Question q = pq.getQuestions().get(0); // This should be your question.
}