‘Honeycrisp’ is a relatively new apple cultivar highly susceptible to physiological disorders, such as soggy breakdown. The overall objective of this study was to identify preharvest weather parameters that influence the incidence of soggy breakdown over the different phases of fruit development. Using weather data and evaluation of fruit quality from three sites in Ontario, two sites in Quebec, and one site in Nova Scotia from 2009 to 2011, and data from four sites in Ontario from 2002 to 2006, a model for soggy breakdown incidence (SBI) was developed to predict the level of susceptibility in ‘Honeycrisp’ apples. This model uses primarily two weather variables during the last phase of fruit development [91 days from full bloom (DFB) to harvest] to accumulate an SBI index during the growing season, from full bloom to harvest. Cool (temperature <5 °C) and wet conditions (precipitation >0.5 mm) during this last phase resulted in increased soggy breakdown susceptibility levels. The predictions of the SBI model resulted in 68% of well-estimated cases (threshold of ±5%) (RMSE = 6.45, EF = 0.28, E = −0.04). Furthermore, firmness was linked to soggy breakdown, in addition to weather conditions, revealing a positive effect of high firmness at harvest on the development of the disorder. However, the effect of fruit quality attributes (e.g., internal ethylene concentration, starch index, firmness, and soluble solid content) by themselves, without considering weather conditions, revealed no relationship with the incidence of soggy breakdown.