‘Honeycrisp’ apples are susceptible to bitter pit, a physiological disorder that impacts peel and adjacent cortex tissue. ‘Honeycrisp’ is also susceptible to chilling injury (CI) that can be prevented by holding fruit at 10 to 20 °C after harvest for up to 7 days. This temperature conditioning period reduces CI risk but can enhance bitter pit development. Previous research demonstrated a controlled atmosphere (CA) established during conditioning can reduce ‘Honeycrisp’ bitter pit development without inducing other physiological disorders. The objective of this research was to evaluate the duration of CA needed to reduce bitter pit development. Experiments were conducted in 2014, 2016, and 2017 with fruit obtained from commercial orchards in Washington State and, in 2017 only, Ontario, Canada. Half the fruit were treated with 42 µmol·L−1 1-methycyclopropene (1-MCP) for 24 hours at 10 °C immediately following harvest. The untreated fruit were held at the same temperature (10 °C) in a different cold room. Following 1-MCP treatment, all fruit were conditioned at 10 °C for an additional 6 days, then fruit was cooled to 2.8 °C. During conditioning, fruit were held in air or CA (2.5 kPa O2, 0.5 kPa CO2) established 1 day after harvest, for 1 to 8 weeks, then in air. All fruit were removed from cold storage after 4 months and then held 7 days at 20 °C. Fruit from most orchards/years stored in CA developed less bitter pit compared with fruit stored continuously in air. CA during conditioning also reduced poststorage peel greasiness but CA for 2 weeks or longer enhanced cortex cavity development in some orchard lots. Treatment with 1-MCP did not reduce bitter pit but enhanced development of peel leather blotch and core browning for some orchards/years. 1-MCP–treated fruit slowed the loss of soluble solids content, titratable acidity, and reduced internal ethylene concentration. Results suggest the potential for postharvest management of bitter pit development in ‘Honeycrisp’ apples by CA established during conditioning with minimal development of other postharvest disorders.