Solar energy development is increasing in warm deserts of the southwestern United States, and ecovoltaics has emerged as an approach to maintain ecosystem function within solar facilities while meeting increasing regional energy demands. The Solar Gemini Project, located in the northeastern Mojave Desert, USA, is one of largest photovoltaic facilities incorporating an ecovoltaics approach, including novel installation practices to reduce disturbance to soil and vegetation and solar tracking bifacial photovoltaic panels to maximize energy generation. To further understand the influence of the facility on environmental conditions, we compared microclimate, temperature, and soil moisture in bare soil interspaces between panel arrays inside the facility to undisturbed desert in nearby areas outside the facility from June 2023–February 2025. Our comparisons included different seasons (summer versus winter), soil depth (shallow versus deep), and facility operation (inactive versus active panels with solar-tracking). We found lower solar radiation, wind speed, and evaporative demand inside the facility compared to outside the facility, with greater differences when panels were actively tracking. When panels were active, air temperature inside and outside the facility was similar on average, but was higher inside the facility during the day and lower at night. Soil surface temperature was lower inside the facility due to panel shading in the morning and evening, whereas soil temperature (0–15 cm) was consistently higher inside the facility. Soil moisture was higher inside the facility and did not drop to the low levels observed outside the facility. In total, we found lower evaporative demand, less heat loading, and higher soil moisture inside the Gemini facility, potentially benefitting flora and fauna in the harsh desert landscape. Yet, we also found daytime increases in air and soil surface temperature inside the facility, and persistent increases to soil temperature. These findings highlight the potentially positive and negative environmental changes associated with ecovoltaics solar energy development in warm deserts and provide evidence that can inform the optimization of solar photovoltaics design and management.