Two experiments were conducted to investigate the effects of active- and passive-modified atmosphere packaging (MAP) on respiration rate (RR) and quality attributes of minimally processed pomegranate arils (cv. Wonderful) stored at 5 °C for 12 d. In experiment 1, pomegranate arils were packaged in low barrier bi-axially oriented polyester (BOP) film under active-MA (5 kPa O2 + 10 kPa CO2, 30 kPa O2 + 40 kPa CO2), passive-MA and in clamshell trays. In experiment 2, a high barrier Polylid® film was used with arils packaged under three active-MAs (5 kPa O2 + 10 kPa CO2 + 85 kPa N2; 30 kPa O2 + 10 kPa O2 + 60 kPa N2; 100 kPa N2) and passive-MA. Arils packed in clamshell trays had lowest RR (RCO2) compared to the other MA treatments in experiment 1, ranging from 41.1 nmol kg−1 s−1 on day 3 to 238.8 nmol kg−1 s−1 on day 12. Respiration rate of arils packaged in the high barrier polylid film was significantly affected by MA treatments. At the end of 12 d storage, total anthocyanin content (TAC) in arils was highest for clamshell packages (0.31 ± 0.01 g L−1) and lowest in passive-MAP (0.27 ± 0.02 g L−1). Packaging arils in high O2 atmosphere and 100 kPa N2 significantly lower aerobic mesophilic bacteria counts throughout the storage duration. Based on sensory scores obtained and microbial load, the shelf life for arils packaged in clamshell trays, passive-MA, and high O2 level MA was 6, 9 and 12 d, respectively.