Market access is a key factor in structuring food procurement in rural communities. For groups undergoing subsistence transition, market interactions further transform lifestyle, with direct consequences for their diet and health. The Punan of Borneo and the Orang Rimba of Sumatra in Indonesia represent traditionally hunter-gatherer groups with recent transition histories. In this study, we use a cross-sectional comparative design across these communities (7 groups; 297 participants) to examine the effects of lifestyle transitions on diet and health at the intersection of market integration and subsistence shifts. In particular, we profiled dietary composition, procurement strategies, and the consumption of sugar, cigarettes, and medicine. We then employed linear mixed-effects models to evaluate associations between these variables, transition states, demographic factors, and Body Mass Index (BMI). Results indicate that market integration variably impacts subsistence practices; specifically, it circumvents the need for food cultivation in early-transition communities and substitutes for wild game in late-transition contexts. Both market access and subsistence transition drive dietary shifts along with increased BMI. The latter process affects women more severely than men. Sugar consumption is high across all communities (68.6 g/daily on average), while cigarettes are most consumed by men in early-transition communities (93%); both have significant health implications. Considering the communities, lifestyle transition appears mediated by the interaction of forest degradation, local infrastructure, isolation, government/NGO initiatives, and market access. In sum, subsistence transitions in Indonesia likely occur within the context of and are driven by market access, influencing dietary composition with sex-specific impacts on health.