Marketing melons (Cucumis melo) as convenient fresh-cut products is popular nowadays. However, damage inflicted by fresh-cut processing results in fast quality degradation and food safety risks. The life of fresh-cut produce can be extended by a modified atmosphere (MA), either generated in a package by tissue respiration (a passive MA) or injected by gas flushing (an active MA). This work investigated the effect of passive and active MA formed in packages of different perforation levels on the quality of fresh-cut melons of two genetic groups: C. melo var. cantalupensis, characterized by climacteric fruit behavior, and non-climacteric C. melo inodorus. The best product preservation was achieved in passive MA packages: non-perforated for inodorus melons and micro-perforated for cantalupensis ones. The optimal packages allowed for the preservation of both genotypes for 14 days at 6–8 °C. The major factors limiting the shelf life of fresh-cut melons were microbial spoilage, translucency disorder and hypoxic fermentation associated with cantalupensis melons with enhanced ethyl acetate accumulation. Inodorus melons were found to be preferable for fresh-cut processing since they were less prone to fermented off-flavor development.