With the shift toward smarter and more sustainable energy communities, optimized operation of Semi–Transparent Photovoltaic (STPV) greenhouses in arid climates like Qatar requires integrated management of energy dispatch, battery lifetime, and crop-specific thermal control. Ambient temperature significantly affects crop cultivation and directly influences the long-term performance and lifespan of battery energy storage systems (BESS), which undergo sudden and frequent charging/discharging events. To address these challenges, this paper proposes an interval-analysis-based optimization model formulated as mixed integer linear programming (MILP) to maximize the daily profit of STPV greenhouses. The model incorporates comprehensive BESS management constraints to extend battery lifespan and includes detailed modeling of electricity generation from STPV walls and roofs. Moreover, a novel thermal model is proposed that accounts for thermal inertia and the effects of solar irradiance on greenhouse internal temperature to represent realistic greenhouse conditions integrated with inverter-based HVAC. In addition, a novel agricultural temperature stability index (ATSI) is introduced, combining statistical measures with crop-specific agricultural requirements, and can be customized according to the requirements of different crops. Daily environmental and technical input profiles from Qatar are used to enhance the realism of the model. Simulations were performed across multiple cases and crop types, including sensitivity analyses on key input parameters. Furthermore, the model’s implications for BESS lifespan and long-term economic performance were evaluated. Results indicate that, for tomato cultivation, SoC-aware operation reduced BESS degradation cost by up to 6.6% from $170.12 to $158.83, although grid transaction cost increased from 0.5224 k$ to 0.8327 k$, highlighting the trade-off between battery lifetime preservation and short-term operating cost. Moreover, the inverter-based HVAC improved crop-specific thermal stability by achieving an ATSI of 0.964, compared with 0.833 for conventional thermostat-based HVAC.