In this study, the effect of cold plasma (CP) on the physicochemical and biological properties of red wine was investigated in comparison with the effects of the conventional preservation method and the combined method. In addition, the effect of storage time after the application of each of the analyzed methods was evaluated. The study examined the effects of the different preservation methods on the pH, color, phenolic content, antioxidant activity and microbiological purity of the red wine. Chemometric analysis was used to discover the relationship between the preservation method used and wine quality. In the wine samples tested, a reduction in phenolic compounds and a decrease in antioxidant activity were noted after storage. This effect was mildest for preservation methods with the addition of potassium metabisulphite and those in which a mixture of helium and nitrogen was used as the working gas. On a positive note, the CP treatment did not affect the color of the wine in a way perceptible to the consumer: ∆E*—1.12 (He/N2; 5 min). In addition, the lowest growth of microorganisms was detected in the CP-treated samples. This indicates the potential of cold plasma as an alternative method to the use of potassium metabisulfite in wine production, which may contribute to its wider use in the alcohol industry in the future.