Agricultural production in arid climates faces challenges due to harsh conditions, requiring cooling technologies to support crop growth. Mechanically active cooling systems, such as heating, ventilation, and air-conditioning, are effective but energy-intensive, leading to high costs. This study proposes using spectrum-selective fluids in greenhouse roofs to supplement the cooling system by blocking near-infrared radiation while allowing photosynthetic active radiation to pass. This approach decreases cooling demand but also reduces yield, presenting a trade-off in greenhouse performance. A stochastic techno-economic analysis was conducted using an integrated input-yield model with historical solar irradiance and temperature data. Scenarios were generated and reduced using k-means clustering. Monte Carlo simulations were used to evaluate the techno-economic performance of the ATO-WO3 greenhouse system under uncertainty. Key indicators assessed included the expected net present value, minimum selling price, and discounted payback period. Although the ATO-WO3 greenhouse exhibited a lower expected tomato yield, 5.87% and 11.55% less than that of the water-based and conventional greenhouse systems, respectively, it outperformed in terms of economic viability. The ATO-WO3 system achieved an expected net present value of $1465.07 m-2, a minimum selling price of $2.25 kg-1, and a discounted payback period of 8.22 years. In addition, a sensitivity analysis was conducted to quantify the influence of key input variables on these techno-economic indicators.