Using primary data collected from 560 farm households in Dawuro zone, southern Ethiopia, this study analyzes the gender gaps in food security among male, female, and joint decision-making farm households. It examines the factors inducing gender gaps among the households of those three categories. The results show that female decision-making households have a lower probability of ensuring food-security and a higher probability of being transitionally and chronically food-insecure. Joint decision-making households showed a higher probability of falling into the chronically food-insecure category. The decomposition results show significant gender gaps between male and female decision-making households in terms of food-secure, transitory food-insecure, and chronically food-insecure categories. Overall, both the endowment and return effects account for the gaps; however, the magnitude of the effect from the return is higher than from the endowment on significant gaps in the food-secure, transitory, and chronically food-insecure categories. Hence, there is a need for policies that not only ensure equal levels of productive resources but also help households build their capacity in order to improve both transitory and chronically food insecure situations.