The microbial community dynamics were investigated in this study to understand the spoilage of beef steaks packaged in both modified atmosphere packaging (MAP): 80%O2-MAP (80% O2/20% CO2) and CO-MAP (0.4% CO/30% CO2/69.6% N2). Steaks were stored at 2 °C for 20 days. Meat physicochemical changes and microbial counts were monitored, and the microbial communities were evaluated by high throughput-sequencing. The microbial diversity for both MAP decreased over time and it was more complex in CO-MAP steaks than that in 80%O2-MAP steaks. B. thermosphacta and Pseudomonas spp. were dominant bacteria of 80%O2-MAP steaks but Pseudomonas spp. gradually outcompeted the former from day 10. Leuconostoc, Lactobacillus, Lactococcus, Vagococcus and Serratia dominated alternately in CO-MAP steaks during storage, and Lactococcus eventually became the most common bacteria. Predicted metagenomes indicated a higher microbial amino acid and lipid metabolism level in 80%O2-MAP compared with CO-MAP at day 20, which may contribute to the dramatic physicochemical deterioration of 80%O2-MAP steaks.