In recirculating aquaculture systems (RAS)s, off-flavors and odors, mainly caused by geosmin (GSM) and 2-methylisoborneol (MIB), can accumulate in the flesh of fish from RAS water, reducing the profitability of production. In this study, peracetic acid (PAA) was applied in three application intervals to pump sumps of rainbow trout (Oncorhynchus mykiss) reared in RAS. Using a real-time polymerase chain reaction (qPCR), the potential off-flavor producers were quantified using geoA and MIB synthase genes. Streptomyces was identified as the major GSM producer, and biofilters showed the highest number of potential off-flavor producers. Concentrations of GSM and MIB were analyzed in the circulating water and in the lateral part of the fish fillet. In water, concentrations up to 51 ng L -1 (GSM) and 60.3 ng L -1 (MIB) were found, while in the fillet, these were up to 9.8 ng g -1 (GSM) and 10.2 ng g -1 (MIB), decreasing with increasing number of PAA applications. PAA applications reduced the levels of off-flavor compounds, although this was insufficient to fully prevent the accumulation of GSM and MIB.