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This study examines whether agroecological farming practices, when employed by highly vulnerable households in sub-Saharan Africa, can improve food security and dietary diversity. The research involved a four-year study with 425 smallholder households, selected purposively based on high levels of food insecurity and/or positive HIV status. The households carried out agroecological experiments of their own choosing over a four-year period. Baseline (n = 306) and follow-up (n = 352) surveys were conducted in 2011 and 2013 respectively to assess changes in farming practices, food security, crop diversity and dietary diversity. Longitudinal mixed effects models were used with 203 matched households to estimate determinants of change in food security and dietary diversity at the population level. Qualitative interviews and focus groups were also conducted to provide depth to the survey findings. The findings show that participatory agroecology experimentation increased intercropping, legume diversification and the addition of compost, manure and crop residue amendments to the soil. Intercropping was associated with food security and the use of organic soil amendments was associated with gains in dietary diversity in bivariate analysis. Household food security and dietary diversity increased significantly over a 2-year period. Importantly, multivariate models showed that spousal discussion about farming was strongly associated with increased household food security and dietary diversity. Households who discussed farming with their spouse were 2.4 times more likely to be food secure and have diverse diets. Addition of compost or manure to the soil significantly influenced dietary diversity. These findings indicate that poor, vulnerable farmers can use agroecological methods to effectively improve food and nutritional security in sub-Saharan Africa. The study also highlights how linking agroecology to participatory research approaches that promote farmer experimentation and gender equity also lead to greater health and well-being. The study sheds light on how agroecological approaches can rapidly improve food security and dietary diversity, even under conditions of acute social, health or ecological stress. It draws attention to issues of equity and farmer-led approaches in addressing food security and nutrition.