The aim of the study was the evaluation and mathematical modeling of the effect of active modified atmosphere packaging (MAP), by the incorporation of CO2 emitters in the package, on the microbial stability and shelf life of gutted sea bass during refrigerated storage. Gutted sea bass samples were packaged in modified atmosphere (50% CO2–40% N2–10% O2) with and without CO2 emitters (ACT-MAP, MAP) (gas/product volume ratio 3:1) and stored at isothermal conditions: 0 °C, 5 °C, and 10 °C. The gas concentration in the package headspace (%CO2, %O2) and microbial growth (total viable count, TVC, Pseudomonas spp., Enterobacteriaceae spp., lactic acid bacteria) were monitored during storage. The microbial growth was modeled using the Baranyi growth model, and the kinetic parameters (microbial growth rate, lag phase) were estimated at the tested temperature and packaging conditions. The results showed that the ACT-MAP samples presented significantly lower microbial growth compared to the MAP samples. The growth rate of the total viable count at 0 °C was 0.175 and 0.138 d−1 for the MAP and ACT-MAP sea bass, respectively (p < 0.05). The shelf life of the MAP sea bass at 0–10 °C (based on a final TVC value: 7 log CFU g−1) was extended 4–7 days with the addition of a CO2 emitter in the package. The CO2 concentration in the ACT-MAP samples was stabilized at approximately 60%, while the CO2 in the MAP samples was approximately 40% at the end of the shelf life.