Temperature plays a critical role in performance and stability of anaerobic digestion processes, subject to frequent meteorological fluctuations. However, state-of-the-art modeling and process control approaches for anaerobic digestion often do not consider the temporal dynamics of the temperature, which can influence microbial communities, kinetics, and chemical equilibrium, and consequently, biogas production efficiency. Therefore, to account for anaerobic digesters operating under fluctuating meteorological conditions, the Anaerobic Digestion Model no. 1 (ADM1) is mechanistically extended in this paper to incorporate temporal changes into temperature-dependent parameters by defining inhibition functions for microbial activities using the cardinal temperature model, and accounting for the lag in microbial adaptation to temperature fluctuations using a time-lag adaptation function. Thereafter, given that temperature fluctuations are a significant disturbance, a control framework based on Model Predictive Control (MPC) is developed to regulate the feeding flow rate and to ensure stable production rates despite temperature disturbances without relying on direct temperature control. An adaptive MPC approach is formulated based on a linear input–output model, where the parameters of the linear model are updated online to capture the nonlinear dynamics of the process and frequent changes in the dynamics accurately. In addition, a fuzzy logic system is employed to assign a reference trajectory for the production rate based on the temperature and its rate of change. Integrating this fuzzy logic system with the MPC controller enhances the production rate on warm days and avoids the operational failure in production on cold days. Additionally, to enhance biogas production rates, the feasibility of utilizing a portion of the produced biogas for external heating purposes is also investigated. It is demonstrated that by utilizing the proposed MPC approach, the additional amount of feed for the digester to produce methane required for a self-consumption biogas-fueled heating system can be calculated according to the meteorological variations. This enhances the process performance and stability. Finally, a thermally optimized dome digester semi-buried in the ground, operating under climate conditions of The Netherlands is considered as a case study to validate the extended model in agreement with biological and physicochemical behaviors of real-world applications, and to demonstrate the effectiveness of the proposed control system in handling temperature changes and enhancing performance.