Due to the widescale impact of 212 Action's anti-blasphemy campaign in 2016, there has been a spike in Islamic moral panic discourse and religiously driven vigilante attacks targeting LGBTQ citizens in Indonesia. Simultaneously, gender nonconforming citizens who have gained social recognition, like a segment of transwomen communities called waria, have continued to carve out alternative spaces and subvert anti-LGBTQ discourse. Waria activists in Yogyakarta, for instance, created the world's first trans-led Islamic boarding school in 2008. Despite suffering attacks from Front Jihad Islam members in 2016, the school has managed to reopen and even to expand its services further for waria communities. In capturing the recent trajectory of activism at the waria Islamic boarding school, this article highlights the multifaceted conditions of precarity faced by Muslim waria in Yogyakarta in the wake of the COVID-19 pandemic. Presenting ethnographic data from the summer of 2022, this paper argues that since the pandemic, in addition to demanding the right to practice Islam, Muslim waria activists have increasingly focused on wellbeing (e.g., food sustainability and emergency shelter) in their rights advocacy in Yogyakarta. Merely perceiving the Islamic boarding school as a site of religious activism diminishes a fundamental aspect of its current grassroots efforts, which is to gain access to basic welfare — a key strategy for the survival of LGBTQ citizens in Yogyakarta and beyond. With greater socioeconomic and psychological uncertainties sparked by COVID-19, human rights for waria and what holistic security means for Indonesian LGBTQ citizens, must also be carefully understood through a lens of health, welfare, and wellbeing.