Soft scald is an apple (Malus ×domestica Borkh.) fruit disorder that appears in response to cold storage after about 2–8 weeks. It appears as a ribbon of dark tissue on the peel of the fruit, with occasional browning into the flesh. Several apple cultivars are susceptible to it, including Honeycrisp. The objectives of this study were to examine the cellular microstructure of fruit exhibiting soft scald and determine if any aspect of the peel microstructure at harvest could be indicative of future soft scald incidence. Light and electron microscopy were used to examine the peel microstructure of ‘Honeycrisp’ fruit that were unaffected or affected by soft scald. Tissue with soft scald had brown pigmented epidermal and hypodermal cells, whereas unaffected fruit peel epidermal cells were unpigmented. Cuticular wax of unaffected peel had upright wax platelets or clumps of wax, but peel surfaces with soft scald exhibited flattened granules and were more fragile than that of unaffected fruit. Epidermal cells of fruit with soft scald were more disorganized than that of unaffected fruit. Light microscopy was used to examine peels of ‘Honeycrisp’ fruit from four growing locations and fruit from a ‘Honeycrisp’ breeding population at harvest. ‘Honeycrisp’ and ‘Honeycrisp’ progeny fruit were also stored at 0 °C for 8 weeks and scored for soft scald incidence. Cross-sections of unaffected peel of stored ‘Honeycrisp’ fruit looked similar to that of freshly harvested fruit. No significant correlations were found between soft scald incidence and measured microstructural attributes of ‘Honeycrisp’ fruit at harvest, suggesting that peel microstructure cannot be used to predict possible soft scald incidence after storage.