Oxygen (O₂) plays a vital role in the blue mussel (Mytilus edulis) survival, microbial growth, and volatile organic compounds (VOCs) formation during transport and storage. This study measures the impact of different atmospheres (% CO₂/O₂/N₂): 30/40/30; 40/60/0; and 0/60/40 on blue mussels' spoilage. Quality parameters were monitored at 4 °C for up to 16 days of storage, including headspace composition (% CO₂/O₂), pH, mortality, microbial analysis, and VOCs concentrations. Selected-ion flow-tube mass spectrometry (SIFT-MS) was used for real-time VOCs measurements. At the end of storage, odor activity values (OAVs) were calculated to assess VOCs that contributed to the overall odor profiles (OAV ≥1). Different atmospheres result in a different shelf life in which B60 condition (% CO₂/O₂/N₂: 40/60/0) prolonged the life span of blue mussels for nine days of storage. A total of 23 compounds were identified in packed blue mussels. The evolution of ethanol; 3-methyl-1-butanol; 2,3-butanediol; acetone; 2,3-butanedione; dimethylamine (DMA); dimethyl sulfide; dimethyl disulfide; and methyl mercaptan were associated with mortality and total plate count (TPC >7 log CFU g⁻¹). This study identifies dimethyl sulfide and methyl mercaptan as the primary contributors to malodor of blue mussels at the end of storage (OAVs = 182–66716).