Heat treatment is used in the orange juice industry to neutralize the action of pathogenic microorganisms. However, it can reduce the nutritional value of the juice. Thus, our study assessed the cold plasma treatment as an alternative method against Escherichia coli and Candida albicans in 'Lima' orange juice. Both, plasma and heat treatments, reduced the amount of E. coli in the juice, inactivating 16.72 and 100%, respectively. Plasma did not inactivate C. albicans, but heat treatment inactivated 100%. Plasma and heat treatment increased Hue angle and luminosity (more yellowish juice). Plasma reduced vitamin C, carotenoids, and polyphenols content, while increased flavonoids. Heat treatment reduced the carotenoid content. However, neither heat nor plasma treatment altered the antioxidant activity. The plasma treatment reduced the intensity of color (chroma), the soluble solids content and the acidity ratio, total sugars, and the vitamin C content of juice compared to the heat-treated and control juices. Plasma-treated juice showed increased levels of yellow flavonoids, total phenolics and antioxidant activity until the 12th day of storage.