In this manuscript, we present changes in study design and analytical strategy due to the COVID-19 pandemic for Nen ŨnkUmbi/EdaHiYedo ("We Are Here Now," or NE). NE is a community-based participatory research multi-level randomized control trial using a stepped wedge design to address sexual and reproductive health disparities among American Indian youth. Adaptations in NE's research design, data collection, and analysis due to the COVID-19 pandemic were made based on meetings with tribally based research team members and outside non-Indigenous researchers involved in NE, as well as the study's Community Advisory Board and the Data Safety Monitoring Board. Based on these iterative discussions, decisions were made to: 1) reorganize the sequence of NE's stepped wedge design clusters, and 2) include additional quantitative and qualitative data collection and analysis in the research design that specifically addressed the impact of COVID-19 on the research participants. These adaptations have the potential to foster greater scientific knowledge in understanding how to address unanticipated 3-way interaction effects in randomized control trials with tribal communities. Findings can also contribute to understanding how public health disasters impact sexual and reproductive health among American Indian youth.