One advantage of high-density apple orchard systems is homogeneity in fruit maturity and quality. However, even in modern orchard systems, variation in fruit quality occurs. ‘Honeycrisp’ apple is susceptible to numerous disorders including bitter pit, soft scald, and poor colour development. Heterogeneity in fruit quality and nutrient distribution can lead to variation in fruit storability. Here, we tested the effect of within-canopy position on fruit calcium and potassium concentrations, quality, and disorder development for fruit across nine representative high-density orchards. Calcium concentrations were greater in the upper part of the canopy compared with the lower part. Potassium was more evenly distributed within the canopy. Calcium concentrations and potassium-to-calcium ratios were significantly correlated with mean bitter pit incidence, which was between 20% and 30% in the lower half of the tree and <15% in the upper half. Fruit quality was significantly affected by the position in the canopy and was not constrained to only colour, but also other quality metrics such as dry matter, size, and firmness. Additionally, the internal ethylene concentrations (IECs) of fruit in the upper canopy were approximately 50% of the IECs for fruit from the lower canopy. With an increased emphasis on uniformity and predictability of fruit for long-term storage, these results underscore the importance of understanding variation within the canopy. Even for high-density systems, significant variation in fruit quality can occur and fruit from the upper canopy has lower disorder incidence and higher fruit quality than fruit from the lower canopy.