In the Reformation era, the Religious Courts were integrated in the Supreme Court in order to realize independent judicial power under one roof. It aims to end the dualism of the formation and dual supervision of the Religious Courts under the Supreme Court and the Ministry of Religion. This study discusses differences in views between the Religious Courts, the Ministry of Religion, and the Supreme Court in the process of integrating Religious Courts under one roof. The method used is the historical method with a legislative approach. The historical method consists of four steps, namely heuristics, verification, source criticism, and historiography. The statute approach relates to an analysis of the articles in the legislation. The main source used is the primary archive in the form of minutes of the Draft Law No. 35 of 1999 concerning Judicial Power, Draft Law No. 4 of 2004 concerning Judicial Power, magazines, and contemporary newspapers. The new findings in this article are the pros and cons of the process of integration of Religious Courts due to differences in interests among stakeholders. Thus, it was concluded that the integration factors of the Religious Courts were not limited to the ideal foundation for realizing judicial independence in the frame of reform but were closely related to economic and political aspects. © 2021 Nova Science Publishers, Inc.