Background: Indonesia is undergoing a rapid nutrition transition—a shift in food consumption related to globalization, modernization, urbanization, and economic development—with potentially adverse impacts on diets, health, and the environment. This study sought to understand the perspectives of a multi-disciplinary group of experts on the effects of the nutrition transition on dietary behaviors, cardiovascular disease (CVD) risk factors, and the food environment in Indonesia. Methods: In-depth interviews were conducted online with 27 Indonesian experts, who are either healthcare providers, nutrition researchers, or environmental researchers. Interview question guides were developed based on a socio-ecological framework. We analyzed the data using deductive and inductive approaches. Results: Experts described a disconnect between awareness about and adherence to healthy diets among Indonesians. They highlighted a marked generational divide in food preferences between the younger population (<40y) and older population (40y+), due to the nutrition transition. Experts perceived that the nutrition transition has also resulted in more eating out, which promotes obesity, through the unhealthy menu offerings from restaurants. Experts also implied that traditional diets are no better than modern diets, due to unhealthy cooking practices, especially frying; suggesting that the combination of higher consumption of fast foods and unhealthy cooking practices may have worsened CVD risk factors in the population. Conclusion: Multi-disciplinary experts indicated that the nutrition transition has negatively impacted diets, health, and food environment in Indonesia. Our findings offer potential hypotheses that can be tested using quantitative approaches, to inform policy and the design of programs to reduce the adverse impacts of the nutrition transition in Indonesia.