BackgroundVoices of under-resourced communities are recognised as important yet are often unheard in decisions about healthcare resource allocation. Deliberative public engagement can serve as an effective mechanism for involving communities in establishing nutrition priorities. This study sought to identify the priorities of community members of a South African township, Soweto, and describe the underlying values driving their prioritisation process, to improve nutrition in the first 1000 days of life.MethodsWe engaged 54 community members (28 men and 26 women aged > 18 years) from Soweto. We conducted seven group discussions to determine how to allocate limited resources for prioritising nutrition interventions. We used a modified public engagement tool: CHAT (Choosing All Together) which presented 14 nutrition intervention options and their respective costs. Participants deliberated and collectively determined their nutritional priorities. Choices were captured quantitatively, while group discussions were audio-recorded. A thematic analysis was undertaken to identify the reasons and values associated with the selected priorities.ResultsAll groups demonstrated a preference to allocate scarce resources towards three priority interventions—school breakfast provisioning, six-months paid maternity leave, and improved food safety. All but one group selected community gardens and clubs, and five groups prioritised decreasing the price of healthy food and receiving job search assistance. Participants’ allocative decisions were guided by several values implicit in their choices, such as fairness and equity, efficiency, social justice, financial resilience, relational solidarity, and human development, with a strong focus on children. Priority interventions were deemed critical to supporting children’s optimal development and well-being, interrupting the intergenerational cycle of poverty and poor human development in the community.ConclusionOur study demonstrates how public engagement can facilitate the incorporation of community values and programmatic preferences into nutrition priority setting, enabling a responsive approach to local community needs, especially in resource constrained contexts. Findings could guide policy makers to facilitate more appropriate decisions and to improve nutrition in the first 1000 days of life.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12889-023-15761-1.