Women in rural communities remain the most vulnerable population in accessing agricultural productive resources with dire implications for food security, malnutrition, and poverty. Effective agricultural and food-related policies should be based on a better understanding of the complex inter-relationship of how socioeconomic, demographic, gender, women empowerment, and geographical location indicators simultaneously affect access to agricultural productive resources and food security. The study quantified the level of inequality in access to agricultural productive resources and explored the mechanism through which socioeconomic status mediates the effect of geographic location on food security. This is a community-based cross-sectional study using a multi-stage stratified cluster random sampling design to generate a representative sample of the target population who live in coastal and non-coastal communities. The Gini inequality index, generalized structural equation models, multivariable modified Poisson and Negative binomial regression models were used. The inequality in access to agricultural productive resources was marginally higher among women than in men, higher in the coastal areas than in the non-coastal areas, and higher among women with low empowerment in agricultural production decision-making. The empowerment of women in agricultural decision-making was found to increase with age, as older women were more empowered to make decisions in agriculture. Approximately 17% [95% CI 15.6–18.6] of the population were food-secured (coastal = 13.9%, non-coastal communities = 20.7%). Socioeconomic status mediates the effect of living in coastal versus non-coastal rural communities on food security. To improve food security, the government should prioritize interventions geared toward improving women's access to productive agricultural resources. These interventions must consider gender-specific constraints, poverty alleviation schemes, legal framework, sociocultural factors, and decision-making power.