Fish oil is the main contributor of persistent organic pollutants (POPs) in fish feed. A combination of active carbon filtration and steam deodourization can remove most of the POPs. However, other fat soluble compounds are also removed, thus possibly affecting the nutritional quality of decontaminated fish oils. Sea water–adapted Atlantic salmon were fed 18 months a commercially relevant diet based on either decontaminated or non-treated fish oil until market size. The development of production-related diseases (fin/skin erosion, bone deformity, cataract) and fillet quality parameters (gutted weight, fillet fat soluble vitamin levels and fatty acid composition, colour, gaping, texture and sensory quality) were assessed. No significant differences in growth performances, feed conversion ratio or quality parameters between the two dietary groups were found. The fillet levels of fat soluble vitamins in market size fish remained unaltered, and only marginal differences were observed in fatty acid profiles. There was a significantly lower percentage of deformed vertebrae in the tail region of fish fed the decontaminated fish oil diets, indicating a positive effect of the use of decontaminated fish oil. No apparent negative effects of the use of decontaminated fish oil in Atlantic salmon diets were reported in this study.