This study aimed to identify equivalent processing conditions using ultrasound (US), pulsed electric fields (PEF), and high-pressure processing (HPP) for shelf-life extension and to ensure the safety and quality of Reineta Parda apple puree (AP) in comparison to conventional thermal pasteurization (72 °C/15 s, CTP). The processing conditions were selected to achieve at least 5 log CFU/g inactivation of Escherichia coli. HPP (400 MPa/1 min), US (60 °C, 20 kHz/12 min), and PEF (57.2 °C, 10 kV/cm, 70 bipolar pulses of 8 µs each) reduced E. coli counts by 6.6, 6.1, and 5.8 log CFU/g, respectively, thus achieving the pasteurization status. After processing, HPP samples showed higher levels of total antioxidant activity (DPPH and ABTS) compared to the other samples. HPP and PEF samples showed lower browning degrees than the CTP samples. All treatments ensured indigenous microbial stability (below 1 log CFU/g) for at least 30 days under refrigeration. Principal component analysis showed that the HPP samples increased their similarity to the untreated fresh AP during storage based on the pH, total soluble content and water activity, retaining its fresh-like qualities. HPP and PEF were found to be potential alternatives to the CTP of AP, resulting in a safe, minimally processed product with improved antioxidant activity.