The study aimed to assess bioactive compounds and polyphenoloxidase activity of minimally processed eggplants stored in different atmospheres. Eggplants (Solanum melongena L.; cv. Ciça) were minimally processed (MP), sanitized and treated with a 2% citric acid solution. They were packed in plastic containers (vacuum) of nylon + transparent polyethylene and submitted to modified atmospheres with the following concentrations of gases: control (atmospheric air), vacuum, 4% O2 + 5% CO2,4% O2 + 6% CO2, 4% O2 + 7% CO2, and 4% O2 + 8% CO2, being stored in a cold chamber (5 ± 1 °C and 90 ± 1% relative humidity) for 10 days. The analyses consisted of the total phenolic compounds, total antioxidant activity, flavonoids, and polyphenoloxidase activity. The experimental design was a completely randomized design in a 6 × 6 factorial scheme (treatment vs. storage period). The data were submitted to analysis of variance and a regression analysis was performed for storage time. The active modified atmosphere with 8% CO2 is effective in reducing the polyphenoloxidase activity in minimally processed eggplant. The contents of phenolic compounds and flavonoids of minimally processed eggplant decrease with storage.