Most sweet cherries produced in the US Pacific Northwest and shipped to distant markets are often in storage and transit for over 3 weeks. The objectives of this research were to study the effects of sweet cherry storage O2 and CO2 concentrations on the respiratory physiology and the efficacy of modified atmosphere packaging (MAP) on extending shelf life. Oxygen depletion and CO2 formation by ‘Bing’ and ‘Sweetheart’ cherry fruit were measured. While respiration rate was inhibited linearly by reduced O2 concentration from 21% to 3–4% at 20 °C, it was affected very little from 21% to ∼10% but declined logarithmically from ∼10% to ∼1% at 0 °C. Estimated fermentation induction points determined by a specific increased respiratory quotient were less than 1% and 3–4% O2 for both cultivars at 0 and 20 °C, respectively. ‘Bing’ and ‘Sweetheart’ cherry fruits were packaged (∼8 kg/box) in 5 different commercial MAP box liners and a standard macro-perforated polyethylene box liner (as control) and stored at 0 °C for 6 weeks. MAP liners that equilibrated with atmospheres of 1.8–8.0% O2 + 7.3–10.3% CO2 reduced fruit respiration rate, maintained higher titratable acidity (TA) and flavor compared to control fruit after 4 and 6 weeks of cold storage. In contrast, MAP liners that equilibrated with atmospheres of 9.9–14.4% O2 + 5.7–12.9% CO2 had little effect on inhibiting respiration rate and TA loss and maintaining flavor during cold storage. All five MAP liners maintained higher fruit firmness (FF) compared to control fruit after 6 weeks of cold storage. In conclusion, storage atmospheres of 1.8–14.4% O2 + 5.7–12.9% CO2 generated by commercial MAP, maintained higher FF, but only the MAP with lower O2 permeability (i.e., equilibrated at 1.8–8.0% O2) maintained flavor of sweet cherries compared to the standard macro-perforated liners at 0 °C. MAP with appropriate gas permeability (i.e., equilibrated at 5–8% O2 at 0 °C) may be suitable for commercial application to maintain flavor without damaging the fruit through fermentation, even if temperature fluctuations, common in commercial storage and shipping, do occur.