Background Climate change is expected to decrease food security globally. Many Indigenous communities have heightened sensitivity to climate change and food insecurity for multifactorial reasons including close relationships with the local environment and socioeconomic inequities which increase exposures and challenge adaptation to climate change. Pregnant women have additional sensitivity to food insecurity, as antenatal undernutrition is linked with poor maternal-infant health. This study examined pathways through which climate change influenced food security during pregnancy among Indigenous and non-Indigenous women in rural Uganda. Specific objectives were to characterize: 1) sensitivities to climate-associated declines in food security for pregnant Indigenous women; 2) women's perceptions of climate impacts on food security during pregnancy; and 3) changes in food security and maternalinfant health over time, as observed by women. Methods Using a community-based research approach, we conducted eight focus group discussions - four in Indigenous Batwa communities and four in non-Indigenous communities - in Kanungu District, Uganda, on the subject of climate and food security during pregnancy. Thirty-six women with ≥1 pregnancy participated. Data were analysed using a constant comparative method and thematic analysis. Results Women indicated that food insecurity was common during pregnancy and had a bidirectional relationship with antenatal health issues. Food security was thought to be decreasing due to weather changes including extended droughts and unpredictable seasons harming agriculture. Women linked food insecurity with declines in maternal-infant health over time, despite improved antenatal healthcare. While all communities described food security struggles, the challenges Indigenous women identified and described were more severe. Conclusions Programs promoting women's adaptive capacity to climate change are required to improve food security for pregnant women and maternal-infant health. These interventions are particularly needed in Indigenous communities, which often face underlying health inequities. However, resiliency among mothers was strong and, with supports, they can reduce food security challenges in a changing climate.