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The escalating demand for water, energy, and food, coupled with the imperative for sustainable development, necessitates innovative solutions to address the complex interdependencies within the water–energy–food nexus. In this context, agriculture and photovoltaics (Agri-PV or Agri–voltaics) systems have emerged as a promising approach to promoting sustainable agricultural practices while enhancing energy efficiency and food production. However, limited research, especially on the technical aspects of Agri-PV, has resulted in a knowledge gap regarding how to model and determine the suitability of Agri-PV for different crops based on local conditions. This study presents a novel approach to modeling and simulating Agri-PV systems for various major crops in developing countries, using Uzbekistan as a case study. It provides a blueprint for selecting suitable Agri-PV systems. The research investigates the technical feasibility of Agri-PV technology tailored to Uzbekistan’s agricultural landscape, with broader implications for Central Asia. Employing a systematic methodology, the study begins by selecting appropriate sites and crops for Agri-PV system testing, ensuring the relevance and applicability of the research findings to the local context. Using advanced software tools such as PVSyst, the study accurately calculates photosynthetically active radiation (PAR) values specific to selected crops, bridging a significant knowledge gap and providing empirical data essential for informed decision making. The methodology further incorporates an in-depth analysis of economic and technical considerations in selecting PV modules and inverters, enhancing the scientific accuracy of the study. By strategically modeling Agri-PV systems based on parameters like row density, module distance, and tilt angle, this research aims to optimize the integration of photovoltaic technology with agricultural practices in Uzbekistan. Moreover, this study helps to understand the impact of Agri-PV systems on the water–energy–food nexus, providing valuable insights into the potential benefits and challenges specific to the region. The study identifies the positive impact of Agri-PV on major crops and provides a suitable design and modeling approach for sustainable farming practices.