This paper presents the results of an experiment based on using a Glide-arc type plasma reactor operating at atmospheric pressure for the quality of fresh pressed tomato juice, variety Bekas. The impact of after-glow plasma gas (air) on the physicochemical, microbiological properties and morphology of the product’s samples was investigated. Five groups of juices characterized by different exposure times (30, 60, 120, 300 and 600 s), as well as untreated juice (as control) were used. The juice quality was assessed on days 1, 3, 5, and 10 of refrigerated storage. Significant increases were observed when Cold Atmospheric Plasma (CAP)-treated tomato juice was tested against total soluble solids, pH, lycopene, and vitamin C in comparison to the control treatments. Moreover, changes in the tested physicochemical values during the storage of juice subjected to the action of cold plasma did not progress as quickly as in the case of the control juice. A significant decrease was observed in total plate count, yeast, and mold after 300–600 s CAP treatment. The findings of the current study suggested that CAP treatment is a promising technique that could provide improved quality and stability during the processing of tomato juice with better physicochemical properties and bioavailable nutrients.