Nutrition educators at the University of California Cooperative Extension (UCCE) have been engaging low-income youth in youth-led participatory action research (YPAR) for several years. During COVID-19, these educators transitioned from in-person to online YPAR programming. Delivering the YPAR program online presented challenges but also fostered new strategies and provided benefits. This study assesses the challenges, strategies and benefits of online YPAR programming, and it examines future program implications from the perspectives of both nutrition educators and youth. Qualitative interviews were conducted via Zoom with eight nutrition educators who attempted to implement YPAR programming during the 2020–2021 school year. We used a retrospective Qualtrics survey to gain information from 54 youth participants. We found that online facilitation encouraged the innovative use of technology, which was especially important because it allowed teams to connect with each other during tumultuous times. This online format made meetings easier in terms of planning, documentation and logistics. However, the online format presented particular challenges, such as coping with internet and technology difficulties and trying to sustain authentic engagement among participants without in-person interactions. Consequently, 50% of nutrition educators and 45% of youth respondents said they preferred a mix of in-person and online meetings for future YPAR programming.