Multiple types of flesh browning can occur as storage disorders in ‘Honeycrisp’ apple (Malus ×domestica Borkh.) fruit. Predicting its occurrence is hindered by differing definitions of the types of browning, incomplete understanding of their etiologies, and difficulty in assessing harvest maturity of ‘Honeycrisp’ fruit. In 2013, of ‘Honeycrisp’ fruit grown, harvested over multiple weeks, and stored in Maine, Minnesota, Ontario, and Quebec, only the Quebec fruit developed diffuse flesh browning. A detailed comparison showed that the Quebec fruit differed in size, but not in other quality attributes, from fruit of the other locations. The Quebec fruit experienced lower temperatures during active fruit growth and were increasing in cell size up to harvest. Analyses of climate data from 2009 to 2015 indicated that accumulated growing degree-days (GDD) 50–60 day after full bloom (DAFB) could account for 31% of the variation in diffuse flesh browning, and seasonal GDD <500 are associated with a greater likelihood of injury. Fruit that exhibited diffuse flesh browning had higher magnesium and lower fructose levels than unaffected fruit. As these measurements were made after browning was assessed, the timing of the onset of these characteristics in relation to browning cannot be determined.