Agricultural anaerobic digestion (AD) is an important biotechnology for renewable energy generation, greenhouse-gas mitigation and circular resource recovery. This study investigates the operational performance and microbial ecology of hyper-mesophilic AD (approximately 40–50 °C) compared with mesophilic and thermophilic conditions, with particular emphasis on temperature shifts and feedstock composition. Continuous stirred-tank digesters treating two contrasting agricultural feedstocks were evaluated using physicochemical monitoring, methane-production analysis, viscosity measurements, life-cycle assessment and 16S rRNA sequencing of 92 samples. Temperature changes caused temporary decreases in methane yield, but the digesters generally recovered, demonstrating process resilience. The optimum temperature was 45 °C, which produced higher methane yields than 35 and 55 °C, while also reducing digestate viscosity and heating or mixing requirements. Starch-rich feedstock showed greater sensitivity to high temperature, including propionate accumulation and elevated failure risk at 55 °C, whereas lignocellulosic feedstock maintained greater stability. Microbial analyses revealed a non-monotonic temperature response: 35 and 55 °C supported highly distinctive, specialized communities, while 45 °C hosted a transitional and less differentiated microbiome. Hyper-mesophilic networks were compact, highly connected and dominated by positive interactions, with rare keystone taxa supporting a cooperative core community. Overall, hyper-mesophilic AD offers a promising balance between productivity, stability, energy efficiency and microbial resilience.