Fish side streams are an environmental and economic problem. In this work, pulsed electric fields (PEF) extraction was optimized and used as a new method for their valorization. Sea bass head, skin, viscera, and backbone were used. PEF technology (123-300 kJ/kg, 1-3 kV/cm) improved the extraction of proteins and antioxidant compounds from head and skin, but was not successful for viscera. SDS-PAGE showed that the protein molecular weight distribution was affected by the extraction process, revealing differences between the control and PEF extraction conditions. In addition, the extraction of macro-minerals and micro-minerals were also evaluated. The effect of PEF differed according to the matrix and the mineral studied. Heavy metals were also taken into account, studying the presence of As, Cd, Hg, and Pb in the extracts. PEF pre-treatment reduced the presence of As in skin, viscera, and backbone, ranging from 18.25 to 28.48% according to the matrix evaluated. The analysis of potential antioxidant bioactive peptides showed that the treatment of the sample directly influenced their variety. Additionally, the extracts obtained from the head were found to increase cell viability when tested on SH-SY5Y cells. In conclusion, PEF extraction can be a useful tool for the valorization of fish side streams.