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Jatropha curcas seeds, as an abundant lignocellulosic biomass, offer a highly promising and ideal alternative for producing energy in the form of methane. Use of J. curcas seeds has the potential to significantly bolster the biofuel sector, fostering a more sustainable circular economy. In the current study, different fractions of processed J. curcas seeds were investigated for biogas production. J. curcas seed pressed cake, a by-product of biodiesel production, was subjected to methanolic extraction. The remaining solids, referred to as methanolic residues, yielded more biogas in batch experiments than pressed cake and residues from aqueous and n-hexane extractions. The compounds extracted with methanol inhibited hydrolysis and reduced biogas production by 35.5% compared to the same setup without extracts. In continuous reactors fed with methanolic residues, the highest biogas yield occurred at an organic loading rate (OLR) of 1 g VS L−1 day−1 and a hydraulic retention time (HRT) of 20 days. The relative abundance of acetogenic bacteria was higher in reactors fed with methanolic residues than in those fed with seed pressed cake, seed oil, and whole seed. Jatropha seed oil and whole seed did not inhibit methanogens. A higher relative abundance of methanogenic communities was observed in all reactors at HRT of 20 days compared to those at HRTs at 15 and 10 days. These findings can be used to increase biogas production during anaerobic digestion of J. curcas seed components and suggests a zero-waste biorefinery production route for value added compounds derived from the removal of biogas-inhibiting components.