The objective of this study was to investigate the effects of delayed controlled atmosphere (CA) storage on fruit quality and disorders in temperature conditioned ‘Honeycrisp’ apples. For three consecutive years, ‘Honeycrisp’apples were harvested from the same commercial orchard and conditioned for 4 d at 12-19 °C immediately after harvest. Apples were then held in ambient air at 3 °C for 0, 2, 4, 8, or 14 wk, followed by CA storage (3 kPa O₂ and 1.5 kPa CO₂) at 3 °C for 6 or 7 mo of total storage time. The effect of 1-methylcyclopropene (1-MCP; 1 µL L^-1) was also investigated. Delaying the establishment of CA reduced the incidence of internal CO₂ injury, with or without flesh cavitation. Furthermore, higher incidence of CO₂ injury required longer delay of CA to reduce the disorder. In some years, delayed CA also resulted in increased lenticel breakdown, bitter pit/blotch and greasiness. 1-MCP treatment reduced lenticel breakdown when CA establishment was delayed 4 wk or more. There was variation in fruit firmness among years and durations of CA delay, and some increase in firmness was observed during storage. 1-MCP-treated fruit showed little change in firmness with delayed CA. There was also little effect of delayed CA on internal ethylene concentration (IEC), soluble solids concentration (SSC), and malic acid content. These results suggest that conditioning and delaying CA storage reduces the incidence of internal CO₂ injuries in ‘Honeycrisp’ apples, but the delay may aggravate other disorders.