In 2020, the COVID-19 health crisis affected all regions of the world, not sparing people already vulnerable to other viral epidemics such as HIV or HCV and/or those in precarious or socially marginalized situations. This is particularly the case for drug users or sex workers.Coalition PLUS, a network of associations fighting against HIV and viral hepatitis which defends and promotes the community-based approach, and its partners, have set up a multi-country community-based research project aimed at documenting the impact of the health crisis on the fight against HIV and viral hepatitis (key populations and community workers/activists), as well as the community responses put in place (EPIC survey).The objective of this paper is to reflect on the implementation of this community-based research study during the COVID-19 health crisis, and in particular the unforeseen difficulties to which the community-based research process had to confront and adapt. The goal is to draw lessons on what worked (and what did not work) in order to capitalize on community-based research practices during this pandemic and subsequently, facilitate the implementation of new research projects in similar contexts.