Food waste (FW) represents the largest fraction of municipal solid waste (MSW) and hospital generated waste, and its conventional disposal leads to landfill overuse, greenhouse gas emissions, and leachate generation. Due to its high organic content, FW is particularly suitable for valorization through anaerobic digestion (AD). This study evaluated the effect of substrate physicochemical composition on methane production and digestate quality under mesophilic conditions (35 °C) using hermetically sealed batch reactors over 32 days. Two substrates were assessed: fruit waste (FrW) and a mixture of fruit waste with potato peel residues (FW). Methane yields reached 211 mL/g VS for FrW and 305 mL/g VS for FW. The digestate derived from FW exhibited higher nutrient content. Germination index (GI) assays showed that a 25% digestate concentration produced the greatest stimulatory effect on radish seeds. The results demonstrate that substrate composition plays a key role in AD performance and the agronomic quality of the resulting digestate. Optimized substrate selection enhances methane yields while improving nutrient availability, thereby supporting environmental impact mitigation, renewable energy recovery, and the sustainable production of organic fertilizers for agricultural applications.