Global demand for blueberries has surged in recent years, primarily due to their health benefits. However, blueberries postharvest losses, particularly firmness loss and decay, remain significant challenges. This study applied high concentrations of CO2 (15% and 20%) for 3 days at 1 °C to highbush (Duke) and rabbiteye (Ochlockonee) blueberries to assess their effects on maintaining quality, especially firmness, during low-temperature storage. Various quality parameters were evaluated, including titratable acidity, pH, total soluble solids, weight loss, and decay. The impact of gaseous treatments on firmness was analysed through mechanical parameters and the expression of genes related to cell wall integrity (XTH23, PL8, PG, PM3, EXP4, and VcGH5). The effectiveness of the treatments varied between species. High CO2 levels successfully reduced decay in both cultivars, but only the highbush variety (Duke) showed improvements in firmness. In Duke, CO2 treatments influenced the expression of genes associated to cell wall integrity, such as XTH23, PL8, and GH5. In contrast, the roles of PG and PME in firmness maintenance were minimal, showing no significant differences between treatments. While CO2 did not enhance firmness in Ochlockonee, it effectively reduced weight loss, highlighting the need for tailored postharvest strategies for different blueberry cultivars.