Indonesian religion-based private schools are generally perceived either as highly elitist, targeted for the well-off group, with great school facilities and well-prepared teachers, or largely impover- ished, intended to serve the marginalized, housed in dilapidated buildings, and taught by poorly prepared teachers. The objective reality, however, is much more nuanced than such a dichotomistic view. This paper reports a study to investigate the impacts of officially mandated regulations on two types of private schools, run by Muhammadiyah and Catholic groups in two provinces of Indonesia. Using mixed methods to tap into both quantitative and qualitative data, the study gathered data from 92 schools in the provinces of Yogyakarta and Central Java. The data suggest that the majority of these schools are stifled with unfriendly policies issued by national and local authorities, while still maintaining their capabilities to serve their students.