Background <p>Under-representation of Muslim ethnic minorities and their mistrust in health research are known barriers to achieving digital health equity. Therefore, this study aimed to understand determinants of Muslim communities’ mistrust in digital health research and explore potential approaches to address this and increase their participation in health research.</p> Methods <p>This study employed a constructivist grounded theory design, involving focus groups with Muslim ethnic minorities living in the United Kingdom. We conducted nine focus groups in mosques, co-moderated by a digital health researcher and an Imam.</p> Findings <p>Muslim ethnic minorities had several negative perceptions about digital health research, which were mainly influenced by lack of their awareness about the purpose and conduct of research. They felt excluded from health research and did not perceive taking part as beneficial to them or their community. These were exacerbated by how research findings related to Muslim ethnic minorities in the UK were used or shared in public spaces (e.g., by media outlets or healthcare providers). Participants suggested that Imams and mosques could play a role in addressing these negative perceptions by raising awareness among their communities using digital resources (e.g., bite size videos, social media community groups) and during regular gatherings.</p> Conclusion <p>Negative perceptions about health research are common among Muslim communities, which are further exacerbated by the way research findings related to South Asians are discussed in public spaces. Despite this, there is a potential of building the Muslim community’s trust and improve their participation in health research if health researchers work collaboratively with mosques or Imams and leverage community-based networks and resources.</p>