‘Honeycrisp’ apples were found to be sensitive to injury from O2 and CO2 partial pressures typical of those in controlled-atmosphere (CA) storage. A preliminary study was conducted in 2008 to investigate the effect of the following O2/CO2 partial pressure (kPa) combinations: 1/0, 3/0, 1/3, 3/3, 21/3, 21/0 (air), and 21/0 with 1-methylcyclopropene (1-MCP; 1 μL·L−1) on CA-related injuries of 'Honeycrisp' during storage for 6 months at 3 °C. ‘Honeycrisp’ apples were found to be sensitive to an injury comprised of irregular-edged brown lesions in the cortex occasionally accompanied by the formation of lens-shaped voids. The symptoms are similar to CA-related injuries described for other apple cultivars and often characterized as a “CO2 injury.” Injury severity increased as O2 declined and as CO2 increased and was evident within the first month of storage. During 2009, 2010, and 2011, a study was conducted to evaluate options for avoiding injury during CA storage for this cultivar. Fruit were conditioned at 3, 10, and 20 °C for 5 days and then exposed to the following O2/CO2 partial pressure combinations: 3/0, 3/3, 21/0 (regular air); 3/3 with diphenylamine (DPA) drench (1 g·L−1); and 21/0 with 1-MCP (1 μL·L−1). Injury severity declined as the temperature of the prestorage conditioning period increased; holding fruit for 5 days at 20 °C almost completely eliminated the disorder. The antioxidant DPA also provided nearly complete control of CA injury. 1-MCP, although not studied in conjunction with a modified atmosphere, was found to cause no injury in air storage and may provide an alternative to CA storage and avoid the risk of CA injury for ’Honeycrisp’. The relationship between disorder development and growing degree-days, rainfall, and maturity indexes was studied. Ethylene was the only factor with a significant linkage to the development of CA injury (R2 = 0.35; P = 0.0043). Suggestions for handling of ‘Honeycrisp’ for extended storage are presented.