Background and aims Fish by-products are generally used to produce fishmeal or fertilizers, with fish oil as a by-product. Despite their importance, fish wastes are still poorly explored and characterized and more studies are needed to reveal their potentiality. The goal of the present study was to qualitatively characterize and investigate the antimicrobial effects of the fish oil extracted from Salmo salar waste samples and to evaluate the potential use of these compounds for treating pathogen infections. Methods Salmo salar waste samples were divided in two groups: heads and soft tissues. Fatty acids composition, and in particular the content in saturated (SAFAs), mono-unsaturated (MUFAs) and Polyunsaturated (PUFAs) fatty acids, was characterized through GC/MS Thermo Focus GC-DSQ II equipped with a ZB-5 fused silica capillary tubes column. The antimicrobial activity of the salmon waste oils was evaluated through the Minimum Inhibitory Concentration assay and the antibiotics contamination was determined by Liquid Chromatography with tandem Mass Spectrometry (LC-MS/MS) analysis. All experiments were done at least in triplicate. Results GC/MS analysis has shown the specific fatty acid composition of the salmon waste oils and their enrichment in MUFAs and PUFAs, with special reference to omega-3, -6, -7, -9 fatty acids. Furthermore, our study has highlighted the antimicrobial activity of the fish waste oil samples against two Gram+ and Gram- bacterial strains. Conclusions These data confirm that the fish waste is still quantitatively and qualitatively an important source of available biological properties that could be extracted and utilized representing an important strategy to counteract infective diseases in the context of the circular economy.