Among the sustainable initiatives for renewable energy technologies, anaerobic digestion (AD) is a potential contender to replace fossil fuels. The anaerobic co-digestions of goat manure (GM) with sorghum (SG), cotton gin trash (CGT), and food waste (FW) having different mixing ratios, volumes, temperatures, and additives were optimized in single and two-stage bioreactors. The biochemical methane potential assays (having different mixing ratios of double and triple substrates) were run in 250 mL serum bottles in triplicates. The best-yielding ratio was up-scaled to fabricated 2 L bioreactors. The biodegradability, biomethane recovery, and process efficacy are discussed. The co-digestion of GM with SG in a 70:30 ratio yielded the highest biomethane of 239.3 ± 15.6 mL/gvs, and it was further up-scaled to a two-stage temperature-phased process supplemented with an anaerobic medium and fly ash (FA) in fabricated 2 L bioreactors. This system yielded the highest biomethane of 266.0 mL/gvs, having an anaerobic biodegradability of 67.3% in 70:30 GM:SG co-digestion supplemented with an anaerobic medium. The BMP of the FA-amended treatment may be lower because of its high Ca concentration of 205.74 ± 3.6. The liquid fraction of the effluents can be applied as N and P fertigation. The Ca concentration was found to be 24.3, 25.1, and 6.3 g/kg in GM and GM:SG (TS) and SG solid fractions, respectively, whereas K was found to be 26.6, 10.8, and 7.4 g/kg. The carbon to nitrogen ratio of solid fraction varied between 2.0 and 24.8 for return to the soils to enhance its quality. This study involving feedstock acquisition, characterization, and their anaerobic digestion optimization provides comprehensive information and may assist small farmers operating on-farm anaerobic digesters.