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Abstract The effects of the gas phase surface discharge plasma system with a spray reactor on yeast in 12, 36, and 60°Brix apple juice were evaluated. Results indicated that the number of Zygosaccharomyces rouxii LB cells in 0.5 L of 12°Brix apple juice was reduced by 5.60 log 10 after discharge plasma treatment for 30 min. When the soluble solids content increased from 12 to 60°Brix, yeast inactivation was decreased by 2.55 log 10. After treatment, the pH level of the apple juice only slightly increased, and the titratable acidity and concentration of reducing sugars remained unchanged. The total color differences between the plasma-treated and untreated samples in 12, 36, and 60°Brix apple juice were 9.53, 7.97, and 3.86. Meanwhile, the concentrations of alcohols, esters, aldehydes, and ketones—the main components of volatile compounds showed no significant change (p < 0.05). Industrial relevance Inactivation of microorganisms using nonthermal plasma technology can reduce food costs and minimize changes in food products and is therefore an alternative to heat-based technology. The proposed research showed that the gas phase surface discharge plasma treatment with a spray reactor can effectively reduce Zygosaccharomyces rouxii in apple juice. In addition, the effect of plasma treatment on the color and volatile compounds of the apple juice were determined. This study provided a technical support for the application of plasma technology in apple juice processing. Highlights • Yeast cells were reduced by 3.05–5.60 log 10 after plasma treatment for 30 min. • Increased soluble solids content negatively affected yeast inactivation. • Plasma treatment did not affect titratable acidity and reducing sugar content. • The total color differences in samples were 3.86–9.53 after plasma treatment. • Plasma treatment did not change in volatile compounds, compared with the control. [ABSTRACT FROM AUTHOR]