Anchovies are among the largest fish catch worldwide. The anchovy fillet industry generates a huge amount of biowaste (e.g., fish heads, bones, tails) that can be used for the extraction of several potentially valuable bioproducts including omega-3 lipids. Following the extraction of valued fish oil rich in omega-3, vitamin D3 and zeaxanthin from anchovy fillet leftovers using biobased limonene in a fully circular process, the solid residue (anchovy sludge) was used as starting substrate for the production of biogas by anaerobic digestion. In spite of the unbalanced carbon to nitrogen (C/N) ratio, typical of marine biowaste, the anchovy sludge showed a good methane yield (about 280 mLCH4∙gVS−1), proving to be an ideal substrate for co-digestion along with other carbon rich wastes and residues. Furthermore, the presence of residual limonene, used as a renewable, not-toxic and edible extraction solvent, does not affect the microbial methanogenesis. The results reported in this study demonstrate that anchovy leftovers after the fish oil extraction process can be efficiently used as a starting co-substrate for the production of biogas in a modern biorefinery.