Non-communicable diseases and associated risk factors, such as obesity, are prevalent and increasing in Malaysia. To address this burden and the heightened vulnerability of low-income communities to these risk factors, the Better Health Programme Malaysia conducted a partial-profile discrete choice experiment (DCE) to inform the design of a community-based obesity-prevention programme. The DCE survey was conducted with community members (n = 1453) from three publicly supported low-cost, high-rise flat complexes in urban Kuala Lumpur. In the survey, community members were asked to choose between different sets of potential evidence-based interventions for obesity prevention. Their responses to these choice tasks were analysed to quantify preferences for these different health interventions using a random utility maximization model. Based on these results, we determined participants' relative prioritization of the different options. The most preferred interventions were those that reduced the price of fruit and vegetables; altered cooking practices at restaurants and food vendors to reduce salt, sugar and oil; and offered reward incentives for completing online educational activities. Community members did not prioritize several evidence-based interventions, including changes to product placement or product labelling, suggesting that these effective approaches may be less familiar or simply not preferred by respondents. The DCE enabled the clear articulation of these community priorities for evidence-based interventions that focus on the supply and promotion of affordable healthy foods within the local food environment, as well as community demand for healthier food options.