The objective of this study was to investigate the efficacy of delactosed whey permeate (DWP) treatment on the physico-chemical, microbial and antioxidant compounds of tomatoes stored at 15 °C for 21 days compared with traditional chlorine treatment. Fresh tomatoes were treated with 3 ml/100 ml DWP or 120 mg/l chlorine solutions and packed in perforated polypropylene bags. The results showed that DWP treatment significantly reduced the number of total aerobic counts (∼1.62 log cfu/g) and yeast and moulds (∼1.66 log cfu/g) of tomatoes compared to chlorine during storage. Moreover, the tomatoes treated by DWP remained firmer (22%) than the control fruits and maintained significantly (p < 0.05) higher levels of vitamin C (15%), total phenols (10%) and antioxidant activity (26%) at the end of storage. Sensory scores confirmed that the DWP treated tomato fruits retained a good appearance and overall quality compared to the chlorine treated samples. The aroma and texture attributes were maintained better in DWP treated tomatoes than chlorine treated tomatoes during storage. Therefore, DWP treatment could be used as a potential washing agent for fresh tomatoes to extend the shelf-life and maintain the nutritional quality during storage.