After the reformation era in 1998, Islamic education, either Pesantren or Madrasah, has witnessed significant growth. Unlike during the Dutch, Soekarno, and Soeharto eras, when Islamic education remained marginalized, Indonesia recently houses the biggest Islamic education system where thousands of Pesantren become homes to Muslim children. Nonetheless, the fall of the later regime in 1998 has hitherto marked the prominence of Pesantren education nationwide along with the rise of Salafi-based Pesantren. This article aimed to discover three novel ultra-conservative variants of Salafi-based Pesantren and their contestation against other Islamic organizations promoting social tension and prejudice. Therefore, using a qualitative research method, the study's main aim is to identify how Islamic school institutions develop influenced by the movement of Islamic groups in Indonesia, specifically Islamic boarding schools. In doing so, this study interviewed 190 informants from 39 of 8 provinces. This study unveiled three Salafi-based Pesantren variants: Salafi jihadis, Salafi Wahabi, and Salafi Haraki. These three variants of Salafi gained little attention from previous studies.