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Fishery processing industries generate large amounts of by-products. These by-products come from fish heads, skin, bones, thorns, and viscera. The disposal of these wastes represents an increasing environmental and health problem. Nowadays, there is a growing interest in how to utilize fish materials that are not used for human consumption. Among the different solutions proposed, the use of proteolytic and lipolytic microorganisms represents a green solution for waste valorization. In this work, first we screened several conventional and non-conventional microorganisms for their proteolytic and lipolytic functions. Then, the most promising strains (<i>Yarrowia lipolytica</i> YL2, <i>Y. lipolytica</i> YL4, <i>Bacillus amyloliquefaciens</i> B5M and <i>B. subtilis</i> B5C) were tested on a fish waste-based solution. After 72 h incubation at room temperature, the supernatants obtained using the strains of <i>Y. lipolytica</i> showed the highest degree of hydrolysis (10.03 and 11.80%, respectively, for YL2 and YL4), the strongest antioxidant activity (86.4% in DPPH assay for YL2) and the highest formation of aldehydes (above 50% of the total volatile compounds detected). Hydrolysates of fish waste obtained with <i>Y. lipolytica</i> may be reused in feed and food formulations for their functional and flavoring characteristics.