Overweight/obesity and inadequate fitness in active duty personnel impact the wellbeing of service members and have significant costs for military readiness and budget. ShipShape (SS), the Navy's weight management program, was designed to promote nutritional, behavioral, and exercise education to service members. Although SS is an evidence-based program, about half of those who complete the program pass the Body Composition Assessment (BCA), one part of the Navy's comprehensive Physical Fitness Assessment (PFA). SS may not fully address underlying behavioral, psychological, and emotional barriers that influence poor eating and exercise habits. A novel solution to improve outcomes is to incorporate acceptance and commitment therapy (ACT) to promote mindful awareness of present moment experiences, improve psychological flexibility, and support commitment to behavior change. This paper describes a cohort-randomized controlled trial of ACT-enhanced SS (ACT + SS) compared to the standard SS-only program. Active duty service members referred to the SS program are randomized to receive 8-weekly ACT + SS or SS-only group interventions. Our aims are to: 1) determine the effectiveness of ACT + SS compared to SS-only; 2) examine psychological flexibility as a mechanism underlying intervention response; and 3) explore potential moderators of intervention response. The primary outcome is weight, one of the key components of the BCA; secondary outcomes include Body Mass Index (BMI), body fat %, self-reported BCA results, physical activity, problematic eating, and quality of life. We have designed a cohort-randomized trial with interventions that are pragmatically implemented in a real-life military setting, and outcomes that are immediately relevant to service members and leadership.