Background: Agroecological methods have the potential to impact nutrition and food security, however, to date there is limited research evaluating this approach. Objective: A 5-year participatory research project with farming households in north and central Malawi was designed to train farmers on agroecological practices, alongside raising awareness on nutrition and gender equity. This cross-sectional study aimed to explore the relationships between crop diversity, food security at the household level, and individual diversity for women, within the context of an agroecology, nutrition education, and farmer mentoring program. Methods: Participating farmers were trained in and experimented with different farming methods. These farmers subsequently trained other farmers on these short-term agroecological practices and provided mentorship using community-based educational methods designed to address both household food security and nutrition. In year 4 of the intervention, a cross-sectional survey assessed farm practices, food security, and individual dietary diversity of 851 participating households. Results: Households with lower crop diversity were significantly less likely to be food secure (odds ratios [OR] = 0.829, P < .001). Women in households with higher crop diversity were more likely to have higher individual dietary diversity (OR = 1.120, P < .01), eat vitamin A rich foods (OR = 1.176, P < .01), and legumes, nuts, and seeds (OR = 1.141, P < .01). Conclusions: These findings suggest that within a participatory agroecological training combined with community-based nutrition education with a focus on social equity, crop diversity is associated with less household food insecurity and poorer diet quality for rural farming households. Crop diversity may improve dietary diversity by making nutritious foods more available.