The efficacy of washing and the investigation of alternative sanitizing treatments for the reduction of microbial population are major issues for fresh fish and seafood. Limited work on the effect of alternative washing media on fish, particularly gilthead sea bream, one of the important popular fish species, has been published and no industrial scaling-up has been reported. The objective of this study was to systematically evaluate the effect of surface decontamination treatments on the microbial load of fish and the quality and shelf life during subsequent chilled storage. Citric acid (200 ppm for 0–10 min), lactic acid (200 ppm for 0–10 min), and peracetic acid (0–200 ppm for 0–4 min) were tested as alternative washing media by immersion of gutted gilthead sea bream by evaluating their effect on microbial growth and physicochemical and organoleptic degradation of fish. The results of the study indicated that washing with citric (200 ppm, 10 min) and peracetic acid (200 ppm, 4 min) significantly delayed the growth of spoilage microorganisms (total viable count, Pseudomonas spp., Enterobacteriaceae spp., and H2S-producting bacteria) in gutted fish and extended the shelf life to 18 days at 0 °C, compared to 11 days without washing treatment. Appropriate handling and processing of fish and shelf-life extension may enable longer transportation and thus open new distant markets, as well as contribute to reduce food waste during transportation and storage.