The combustion of fossil fuels is accompanied with a number of alarming problems such as fossil fuel depletion, increase in their prices, and emission of greenhouse gases. Thus, the need for the alternative renewable biofuels was increased to replace non-renewable fossil fuels. The sustainable use of non-edible feedstocks and waste for production of biofuels is a potential approach for reducing dependency on fossil fuels and mitigating environmental pollution. In the current study, the effects of carbon to nitrogen (C/N) ratios on methane yield during anaerobic co-digestion of Jatropha curcas de-oiled seed kernel and mango peels were evaluated in continuous reactors. The biogas potential and effects of acid pretreatment on J. curcas fruit were also evaluated during anaerobic batch digestion. The methane yield of co-digested mango peels and seed kernel (1:4 weight ratio based on volatile solids) was 61%, 50%, 36%, and 25% higher compared with the methane yields of mango peels, seed kernel, mango peels/seed kernel (2:1 w/w), and mango peels/seed kernel (1:1 w/w), respectively. The methane yields of the co-digestion of mango peels and seed kernel at 1:4, 1:1, and 2:1 ratios were 52%, 39%, and 32% of the theoretical yields, respectively, illustrating the importance of adjusting C/N ratio with the right amounts of co-substrate. The biogas yield of pretreated fruit coat was 7%, 22%, 34%, 50%, and 74% higher than that of the seed kernel, fruit coat (non-pretreated), de-oiled kernel plus seed coat (pretreated) (1.7:1, by weight), seed coat (pretreated), and seed coat (non-pretreated), respectively. Additionally, pretreatment of fruit coat and seed coat resulted in 22% and 47% higher biogas yields compared with their non-pretreated counterparts. This study revealed key substrate selection and pretreatment methods for increasing methane production from common seed oil production and agricultural wastes.