Fishery by-products are rich in biologically active substances and the use of green and efficient extraction methods to recover these high-added-value compounds is of particular importance. In this study, accelerated solvent extraction (ASE) and pulsed electric field (PEF) were used as innovative approaches to recover extracts from rainbow trout and sole side streams rich in high-added-value compounds. Then, evaluate the heavy metals, proteins and their antioxidant capacity. The impact of the obtained extracts on bacterial growth and anti-inflammatory potential was evaluated. The results showed that some extracts could inhibit the growth of pathogenic bacteria, including the ASE rainbow trout skin and the PEF sole viscera extracts, which showed a significant antibacterial activity on Staphylococcus aureus. The PEF sole viscera extract also showed an inhibitory effect on the growth of Salmonella. Some extracts promoted probiotic bacteria growth, including the PEF rainbow trout head and skin extracts promoted Lactobacillus casei growth, while the ASE rainbow trout head and skin extracts promoted Bifidobacterium lactis growth. Even more, some extracts have potential anti-inflammatory properties, such as ASE-rainbow trout-viscera extracts, PEF-sole-skin extract. Therefore, the use of ASE and PEF can be considered as useful strategies to recover antimicrobial, prebiotic and anti-inflammatory extracts from rainbow trout and sole side streams although it is necessary to evaluate the one by one each specific side stream.