We present an optimized non-thermal atmospheric plasma (NTAP)-based reaction-discharge system that was applied for a continuous-flow treatment of apple juice (AJ). To optimize this system for a high-throughput production of AJ with ameliorated properties, the effect of several parameters was studied using design of experiments approach followed by the response surface methodology. Additionally, nutritional, physicochemical, microbiological and cytotoxic properties of resulting AJ were assessed. It was established that NTAP treatment of AJ led to rise in concentration of Ca, Fe, K, Mg, Na and Sr by 8–10% as well as Al, B, Ba, Cu, Mn and Zn by 11–15%. Additionally, the increased total phenolic content by ~ 11% in addition to the prolonged by up to 12 days shelf life of the product were observed. Moreover, it was found that the NTAP-treatment of AJ did not change the structure of organic compounds present in AJ, in addition to its °Brix value, color and ferric ion reducing antioxidant power. Furthermore, AJ subjected to NTAP did not show any cytotoxic activity towards non-malignant human intestinal epithelial cells but exhibited induced cell cytotoxicity in human colorectal adenocarcinoma cells. Our study provided arguments for future introduction of these types of preparations to the global market.