In developing countries, governmental programs push agricultural supply chain networks to optimize farmer food security and rural growth. Decision-making in this system includes available cropping options and criteria regarding nutrition, income, work capacity that must be satisfied. We propose a mathematical optimization model to help the decision-making, tested in a case study: Caazapá-Paraguay, where the rural population is 80%, and 42% is poor. The optimization model addresses the problem complexity, suggests the crops, improves the production and rotation mix, decreases the total cost, and satisfies almost the same nutritional requirements.