Photovoltaic greenhouses have emerged as a promising solution to enhance the energy sustainability of protected agriculture by simultaneously enabling crop production and on-site renewable energy generation. This approach is particularly relevant in high-altitude tropical regions, such as the Bogotá Savanna, where solar availability is relatively stable throughout the year and energy costs represent a significant operational constraint. However, the integration of photovoltaic systems introduces shading effects that can alter the internal microclimate, making it necessary to assess their impacts on thermal conditions, airflow patterns, and overall environmental suitability for crop growth. This study presents an integrated assessment of microclimatic behavior and energy performance of a photovoltaic greenhouse using computational fluid dynamics (CFD) simulations coupled with a solar energy generation analysis. A three-dimensional CFD model was developed to evaluate the spatial distribution of air temperature, airflow velocity, and ventilation patterns under three different photovoltaic shading levels applied to the greenhouse roof. Boundary conditions were defined using representative climatic data for the Bogotá Savanna, allowing the simulation of realistic operating scenarios. In parallel, the electrical energy generation potential of the photovoltaic system was estimated based on local solar radiation conditions, enabling an evaluation of the balance between microclimate modification and energy production. The results highlight that photovoltaic shading significantly influences the internal thermal stratification, air circulation, and microclimate uniformity. Moderate shading levels contribute to reducing excessive thermal loads while maintaining adequate ventilation, whereas higher shading intensities may lead to localized temperature gradients and reduced air movement. From an energy perspective, the photovoltaic system demonstrates a meaningful capacity to supply a portion of the greenhouse’s energy demand, supporting self-consumption strategies. Overall, the findings demonstrate that the combined use of CFD modeling and energy analysis provides a robust framework for optimizing photovoltaic greenhouse designs, facilitating informed decision-making that balances crop microclimate requirements with renewable energy generation in high-altitude tropical environments.