Racism persists, underscoring the need to rapidly document the perspectives and experiences of Black, Indigenous and People of Color (BIPOC) groups as well as marginalized populations (eg, formerly incarcerated people) during pandemics. This methods paper offers a model for using Public Health Critical Race Praxis (PHCRP) and related critical methodologies (ie, feminist and decolonizing methods) to inform the conceptualization, methods, and dissemination of qualitative research undertaken in response to the evolving COVID-19 pandemic. Using purposive snowball sampling, we identified organizations involved with health equity and social justice advocacy among BIPOC and socially marginalized populations. Focus group participants (N=63) included community members, organizers, activists, and health workers. We conducted topic-specific (eg, reproductive justice) and population-specific (eg, Asian and Pacific Islander) focus groups (N=16 focus groups) in rapid succession using Zoom software. A self-reflexive, iterative praxis guided theorization, data collection and analysis. We obtained community input on study design, the semi-structured discussion guide, ethical considerations and dissemination. Applying PHCRP, we assessed our assumptions iteratively. We transcribed each interview verbatim, de-identified the data, then used two distinct qualitative techniques to code and analyze them: thematic analysis to identify unifying concepts that recur across focus groups and narrative analysis to keep each participant's story intact. The praxis facilitated relationship-building with partners and supported the iterative assessment of assumptions. Logistical constraints included difficulty ensuring the confidentiality of virtual discussions. These novel approaches provide an effective model for community-engaged qualitative research during a pandemic.