This study estimates agricultural residue biomass available for biogas generation in smallholder farming systems in the rural Vakinankaratra region of Madagascar, during 2017–2018. Estimations of biomass were done using a combination of agricultural household surveys, literature models, and publicly available data. Manure from four types of farm animals and 17 residue types from ten crops were assessed. In the studied period, gross biomass produced from animal manure and crop residue were 19.4 ± 7.41 and 7.3 ± 1.08 tonnes fresh weight per year per agricultural household, respectively, of which up to 54% and 83% are estimated as recoverable for the production of bioenergy in the studied area, respectively. Estimations indicate that available animal manure and crop residue have the potential to generate 291 ± 92 and 745 ± 122 Nm3 of methane per year per agricultural household respectively, equivalent to 10.5 ± 3.34 and 26.8 ± 4.28 GJ of heat energy from manure and residues, respectively. Theoretically, the average estimated energy potential can result in the complete substitution of domestic fuels in agricultural households. Approximately 0.12 tonnes of nitrogen per household per year can be recovered from the estimated digestate (using all residue types) after energy recovery, which can be employed for crop fertilization. The recovered nitrogen corresponds to 0.26 tonnes urea fertilizer per household per year. The investigation shows that anaerobic digestion based on crop residue and manure has the potential to meet a significant portion of energy needs of smallholder farmers in the Vakinankaratra region of Madagascar and can make an important contribution to providing fertilizer for on-farm use.