Apples are one of the most important fruit in the worldwide scenario and highly vulnerable to storage disease. Postharvest diseases cause significant economic losses in apple production, estimated to range from 30 to 40% in developing countries, reaching 60% in more extreme cases. The goal of this study was to evaluate fungal and patulin contamination, besides its correlation with the volatile compounds (VCs) in ‘Maxi Gala’ apples (up to 25% decayed) under controlled atmosphere (CA) and dynamic controlled atmosphere with respiratory quotient (DCA-RQ) of 1.3 and 1.5 combined to different partial pressures of carbon dioxide (pCO2). Fruits were stored over nine months under the above-mentioned conditions, at 2.0 °C, plus seven days shelf life at 20 °C. Fungal toxigenic species and patulin accumulation were found in decayed apples from all treatments. Penicillium expansum was the most prevalent species. DCA-RQ1.3 + 0.4 kPa CO2 had the highest Penicillum sp. and P. expansum concentration (2.7 log CFU/g) and, in the opposite, lowest patulin accumulation (95 μg kg−1), evidencing a lack of correlation between fungal counts and mycotoxin accumulation. DCA-RQ1.5 + 1.2 kPa CO2 provided the highest patulin contamination (440 μg kg−1). All fruit showed patulin contamination higher than the maximum patulin limit allowed in most countries’ regulations (50 μg kg−1). It was observed that fungal growth can also contribute to changes in the volatile’s composition. A total of 103 VCs were identified. Acids, alcohols and aldehydes were the groups with compounds found in higher concentrations. Styrene and 3-methyl-1-butanol are considered P. expansum markers in some apple cultivars and were detected in the samples. DCA storage conditions with lower CO2 concentration was associated with least patulin concentration consequently being a better storage condition for this cultivar. This is an important point that deserves further investigation.