Abstract Background Exposure to gestational diabetes mellitus (GDM) is associated with increased risk for type 2 diabetes (T2DM) in mothers, and poor cardiovascular health among offspring. Identifying effective methods to mitigate T2DM risk has the potential to improve health outcomes for mothers with a history of GDM and their children. The goal of the EPIC El Rio Families Study is to implement and evaluate the effects of a 13-week behavioral lifestyle intervention on T2DM risk factors in at-risk mothers and their 8- to 12-year-old children. We describe herein the rationale for our specific approach, the adaption of the DPP-based curriculum for delivery to patients of a Federally Qualified Health Center (FQHC), and the study design and methodology. Methods The effects of the intervention on reduction in excess body weight (primary outcome), hemoglobin A1c, blood pressure, and changes in lifestyle behaviors associated with weight trajectory and T2DM risk in mother-child dyads will be evaluated during a 13-week, group randomized trial wherein 60 mothers and their children will be recruited to the intervention or wait-listed control conditions at one of two FQHC locations. Intervention participants (n = 30) will begin the group program immediately, whereas the wait-listed controls (n = 30) will receive a booklet describing self-guided strategies for behavior change. Associated program delivery costs, acceptability of the program to participants and FQHC staff, and potential for long-term sustainability will also be evaluated. Discussion Successful completion in our aims will produce a scalable program with high potential for replication and dissemination, and estimated intervention effects to inform T2DM prevention efforts on families who use the FQHC system. The results from this study will be critical in developing a T2DM prevention model that can be implemented and scaled across FQHCs serving populations disproportionately burdened by T2DM. Trial registration ClinicalTrials.gov NCT03781102; Date of registration: 19 December 2018.