Initial short-term storage is a treatment where fruit are cooled to 33 °F for a specific time period and then moved to 38 °F until the end of storage. Its effects on the development of physiological disorders in ‘Honeycrisp’ apples (Malus domestica) were investigated for two seasons. During the first season, fruit were harvested from two orchards and stored at 33 and 38 °F, with and without 1 week of conditioning at 50 °F, or stored for 4 weeks at 33 °F followed by 4 weeks at 38 °F. All fruit were stored for a total of 8 weeks. In the second season, fruit were harvested from one orchard and stored at 38 °F either with or without 1 week of conditioning at 50 °F, or stored for 1 week at 33 °F and moved to 38 °F for 15 weeks followed by 7 d at 68 °F. Short-term storage (1 to 4 weeks) at 33 °F decreased bitter pit for all orchards in the two seasons, except in comparison with the continuous 33 °F storage in the first season; soft scald was also reduced in the first season compared with continuous storage at 33 °F, with higher incidence of soft scald in orchard one compared with orchard two. Initial short-term storage at 33 °F resulted in lower soggy breakdown incidence compared with storage at 33 °F with 1 week of conditioning at 50 °F for fruit from orchard two in the first season, the only year when low-temperature injuries were observed. In conclusion, initial short-term storage at 33 °F followed by storage at 38 °F maintained the highest percentage of healthy fruit in the two seasons.