The scope of this work is to compare cow’s milk hygienization methods (pasteurization, sterilization, and cold plasma treatment) in terms of milk’s toxicological safety (using Danio rerio larvae), microbiological safety (counts of mesophilic aerobic bacteria, yeasts, and molds), nutritional properties (polyphenols, vitamins: B1, B2, B3, B5, B6, B9, and B12, minerals: Ca, Zn, Se), physicochemical properties (pH, conductivity, particle size, color), colloidal stability (turbidimetric method), and chemical changes in milk samples at the molecular level (FT-IR). Pasteurization was performed at 65 °C for 30 min, sterilization at 110 °C for 30 min in an autoclave, while cold plasma treatment was carried out in a gliding arc reactor using nitrogen or air as the working gas for 5, 10, or 20 min, ensuring that the milk temperature was kept below 36 °C. The studies showed that milk preserved with plasma is toxicologically safe and microbiologically safer than fresh milk. Plasma-hygienized milk also retains a higher concentration of vitamins and minerals than temperature-hygienized milk samples and has physicochemical properties similar to those of fresh milk. The use of a gliding arc reactor for milk treatment is important for potential industrial implementation.