The implementation of the circular economy and green energy transition for the treatment of agricultural waste into bioenergy presents greater challenges in mountainous and rural areas. The integration of rural-farming plant (tomato plant residue, TR; and cacao pod husk, CPH) and animal-based biomass waste (deer manure, M) with an anaerobic digestion (AD) plant as a substrate has the potential to produce biohydrogen and biomethane as a source of bioenergy in rural farming areas. This study aims to investigate the potential of these feedstocks, including mono- and co-digestion of M and TR in single-stage AD. The co-digestion of M and TR significantly enhanced the biogas and methane production performances, with an increase of 27.5–173.2% compared to mono-digestion. The ratio of M to TR affects the total solid (TS) load in the initial AD process. A TS greater than 3% was found to be more favorable for methane production. This co-digestion method avoids the accumulation of volatile fatty acids (VFAs) in the mixture which prevents inhibition of methane production. The effect of initial substrate and inoculum concentration in two-stage AD using dried CPH powder was also explored in this study. The acidic thermochemical pretreatment of CPH has been demonstrated to significantly enhance biohydrogen production. The optimal biohydrogen and methane production using CPH in two-stage anaerobic digestion was achieved by a substrate concentration of 12 g Volatile Solidadded/L and an inoculum concentration of 10% v/v (volume/volume). According to this study, all residue generated by the agricultural sector has the potential to be utilized with greater added value within the agricultural industry to support the green energy transition in rural farming areas.