Microbial contamination during seafood processing can often lead to a reduction in shelf life and the possibility of food-borne illnesses. Sanitisation with chlorine-based products during seafood processing is therefore sometimes undertaken. This study compared the effects of two sanitisers, chlorine dioxide (ClO2) and hypochlorous acid (HOCl) at their suggested concentration (5 ppm and 10 ppm; 50 ppm and 100 ppm respectively), on physical, chemical, and microbial qualities of Atlantic salmon (Salmo salar) fillets throughout 7 days of simulated retail display refrigeration. Parameters used for assessment included quality index (QI), drip loss, colour, texture, histology, total volatile base nitrogen (TVB-N), lipid oxidation (malonaldehyde, MDA), pH, and total viable count changes. Results indicated that whilst drip loss increased over the storage time, day 4 and 7 drip loss in both sanitisers decreased significantly compared with the control. There was a linear relationship (R > 0.70) between QI and storage time in all treatments, particularly in regard to skin brightness, flesh odour, and gaping parameters, but treatment differences were not present. Texture parameters including gumminess, chewiness, and hardness increased over time in the control whilst both sanitiser treatments seemed to provide protective effects against texture hardening during storage. The observed softening effects from the sanitiser treatments were aligned with microstructural and cytological changes in the histology results, as evidenced by a reduced fibre–fibre adhesion, myodigeneration, and an increase in interfibrillar space over storage time. Colour, especially chroma (C*), was shown to decrease over time in control, whereas insignificant protective effects were observed in both sanitiser treatments at day 7. Irrespective of treatment and storage time, MDA levels exceeded the acceptable limit on all days, whilst TVB-N levels were below the critical limit. Although pH was influenced by treatment and storage time, the pH was within the normal range. Microbiological results showed that with sanitiser addition, TVC was below the permissible level (106 CFU/g) until day 4 but ClO2 ice (5 ppm), ClO2 (10 ppm), and HOCl (100 ppm) treated fillets all exceeded the limit on day 7. The mixed results on the effect of sanitiser addition on fillet quality and shelf life suggested that further investigation on pathogen reduction, sanitiser introductory method, as well as testing the same treatments in low-fat fish models would be recommended.