A Quality Index Method (QIM) scheme was developed for modified atmosphere packaging (MAP) packed gilthead seabream, and the effect of MAP gas mixtures (60% CO2 and 40% N2; 60% CO2, 30% O2, and 10% N2), temperature (2, 4, and 8 °C), and time of storage on QI scores was assessed. QI scores were crossed with sensory evaluation of cooked fish according to a modified Torry scheme to establish the rejection point. In order to reduce redundant parameters, a principal component analysis was applied on preliminary QIM parameters scores coming from the best performing MAP among those tested. The final QIM scheme consists of 13 parameters and a maximum demerit score of 25. The maximum storage time was found to be 13 d at 4 °C for MAP 60% CO2 and 40% N2. Storage at 2 °C do not substantially improved sensory parameters scores, while storage under temperature abuse (8 °C) accelerated drastically the rate of increase of QI scores and reduced the maximum storage time to 6 d.