Throughout its development, in order to avoid intellectual stagnation within formal study programs, learning activities at Pesantren al-Risalah li al-Dirasah al-Islamiyyah have placed greater emphasis on alternative studies in Islamic thought and scholarship. As an example, since 2018 the pesantren has engaged in collective discussions of al-Muqābasāt by Abu Ḥayyān al-Tawḥīdī.
Following a brief period of inactivity due to the COVID-19 pandemic, the pesantren began to revitalize its activities in 2022 by strengthening existing programs while simultaneously introducing new alternative discourses. In 2024, Pesantren al-Risalah further reinforced its institutional existence by establishing a foundation (yayasan) to formally oversee its operations and by applying for official authorization from the Ministry of Religious Affairs. The primary objective of this development is to ensure the sustainability of pesantren-based activities, particularly the study of Islamic sciences in accordance with the curriculum of the salafiyah pesantren tradition.