A pre-harvest apple (Malus × domestica Borkh.) disorder named “green spot” (GS) was recently identified on ‘WA 38’ apples. Previous work indicated a tentative association between GS and fruit mineral imbalance, and an influence of rootstock selection on GS frequency; however, the specific causes, risk factors, and mitigation steps have not been explored. In this study, the role of microclimate, modified using netting or fruit bagging, on GS incidence in ‘WA 38’ apples over two years on two different dwarfing rootstocks, ‘Geneva 41’ (‘G.41’) and ‘Malling 9-Nic29’ (‘M.9’), was investigated. Early season fruit bagging reduced GS appearance, but netting showed mixed results between year and rootstock. Rootstock selection influenced GS incidence, especially in the 2021 season. Fruit mineral analyses highlighted some differences of mineral composition between symptomatic and asymptomatic apples, which helped to corroborate earlier reports; however, within the full context of these results, it is not clear that nutrient imbalance directly influences disorder incidence. Further work to understand the mechanisms behind GS emergence should consider environmental factors, including light, humidity, and wind, as well as anatomical features of ‘WA 38’ fruit, such as lenticel morphology and physiology.