The research material consisted of not from concentrate (NFC) apple juice, which underwent innovative processes of spray deaeration and flow microwave pasteurization. Traditional commercially available pasteurization was the control. Deaeration was conducted at two different temperatures (25 °C and 50 °C) and three rotational speeds of the spray disc (150 rpm, 450 rpm, 750 rpm). Flow microwave pasteurization was carried out at 90 °C with a flow rate of 5.8 L/min. Deaeration at a temperature of 25 °C and a rotation speed of 150 rpm resulted in a significant reduction in oxygen levels in the juice to 0.9 mg/L. Microwave pasteurization led to an almost 100% reduction in oxidoreductases activity (PPO, POD). Immediately after the process, microwave-pasteurized juice exhibited better stability of the total polyphenol content, with a TPC of 73.8 mg/100 mL. Microwave pasteurization caused a threefold increase in antioxidant capacity (176.8 µM/100 mL) compared to fresh juice. The color of microwave-pasteurized juice was more appealing than that of traditionally pasteurized juice.