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Applying the dormitory system for thousands of santri (student of Islamic boarding school in Indonesia), Quranic pesantren (Islamic boarding school) has been considered as one of the main culprits in the spread of the coronavirus disease 2019 (COVID-19). Such assumption is created solely from the applicable health protocols and protective measures to avoid COVID-19 transmission in pesantren. As a matter of fact, pesantrens are known to have applied a distinctive way of coping with COVID-19. This study aims to elucidate the theology of health of Quranic pesantren in the face of COVID-19. Research data were generated through observational method on three Quranic pesantrens in Yogyakarta, interviews with caregivers, the COVID-19 task force of the pesantren, santri and documentation related to the handling of COVID-19 in the three pesantrens. The results showed that the Quranic pesantren as a subculture has a distinctive way of dealing with COVID-19 pandemic by integrating modified health protocols in accordance with the actual conditions of the pesantren and by applying rituals of Islamic spirituality by reciting verses of the Qur’an, salawat (prayers for the Prophet), prayers and hizib (prayer for salvation and rejecting calamities). Three pesantrens chose these methods by drawing on the belief that COVID-19 is God’s creature and, thus, it only works on God’s orders and will stop if God wills. In line with this, this study suggests a method for handling COVID-19 by not only emphasising the health protocols and medical procedures but also taking into account the importance of local wisdom. Contribution statement: This article contributes to the strategy of COVID-19 handling by combining the health protocols of COVID-19 and the applicable local wisdom, such as religious ritual as practiced by numerous pesantren in Indonesia.