Even though the UN's Sustainable Development Goals emphasize improving dietary diversity and overall nutritional status globally by promoting sustainable agriculture, inadequately diversified dietary intake remains a public health problem in many low-income countries, including in Sub-Saharan Africa. The main objective of this study was to gather relevant information to gain an improved understanding of household dietary diversity and explore the role that production diversification could play within household diets and nutrition so that appropriate interventions could be implemented with the goal of enhancing nutrition-sensitive agriculture while also considering the varied features across the agroecosystems. Agroecosystem-based cross-sectional study design was employed. Data were collected predominantly through semi-structured questionnaires and analyzed by descriptive and inferential statistics, and a multilevel mixed-effect model. Results showed that the usual dietary intake of households has a monotonous pattern dominated by starchy staple foods, and consumption of fruits, vegetables, and animal-sourced foods was very limited. One out of five households had inadequate dietary diversity but varied significantly across agroecosystems. About 26% of the heterogeneity in dietary diversity was attributed due to agroecosystem level factors. In the fixed-effect part of the model, production diversification, wealth status, number of meals per day, market access, and annual mean rainfall were significantly associated with household dietary diversity status. The findings of our research contribute to give insights on the linkage between dietary diversity and production diversification among subsistence rural farmers across contrasting agroecosystem zones. Therefore, understanding agroecosystem variations and local context in the rural subsistence farming setup is a key point in designing nutrition-sensitive agriculture.