Understanding the deep meanings of the Qur'an and bridging the language gap between modern standard Arabic and classical Arabic is essential to improve the question-and-answer system for the Holy Qur'an. The Qur'an QA 2023 shared task dataset had a limited number of questions with weak model retrieval. To address this challenge, this work updated the original dataset and improved the model accuracy. The original dataset, which contains 251 questions, was reviewed and expanded to 629 questions with question diversification and reformulation, leading to a comprehensive set of 1895 categorized into single-answer, multi-answer, and zero-answer types. Extensive experiments fine-tuned transformer models, including AraBERT, RoBERTa, CAMeLBERT, AraELECTRA, and BERT. The best model, AraBERT-base, achieved a MAP@10 of 0.36 and MRR of 0.59, representing improvements of 63% and 59%, respectively, compared to the baseline scores (MAP@10: 0.22, MRR: 0.37). Additionally, the dataset expansion led to improvements in handling "no answer" cases, with the proposed approach achieving a 75% success rate for such instances, compared to the baseline's 25%. These results demonstrate the effect of dataset improvement and model architecture optimization in increasing the performance of QA systems for the Holy Qur'an, with higher accuracy, recall, and precision.