The sidestreams produced during fish processing end in a separation tank where the resulting fractions follow biogas production or wastewater treatment. These streams can alternatively be used for production of protein-rich fungal biomass for e.g. fish feed applications, a product in increasing demand. These streams and upper streams originated during fish processing were used in this study for production of biomass using the edible filamentous fungus Rhizopus oryzae. The COD of the streams varied between 11 and 54 kg/m3 and, after fungal conversion of organic matter into protein-rich biomass and separation, a reduction of 34–69% was achieved. The stream origin had an effect on the final production and composition of the fungal biomass: 480 kg of biomass containing 33% protein per ton of COD were produced after cultivation in the separation tank streams, while 220 kg of biomass containing 62% protein per ton of COD were produced in upper sidestreams with lower amounts of suspended solids. Changing the initial pH (6.1–6.5) to 5.0 had a negative influence on the amount of biomass produced while medium supplementation had no influence. Thus, fish processing sidestreams can be diverted from biogas production and wastewater treatment to the production of protein-rich biomass for feed applications.