The chemical composition, sugars profile, total phenolic compounds, phenolic profile and antioxidant activity of ‘Golden Delicious’ apples during storage under controlled atmospheres were evaluated. Total lipids and proteins slightly decreased during storage, while total carbohydrate and mineral content remained constant. The content of total phenolic compounds ranged from 564–748 mg gallic acid equivalents per 100 g of dry apple. Epicatechin, chlorogenic acid, catechin, phloridzin, cyanidin-3-galactoside, quercetin-3-galactoside and quercetin-3-glucoside were the seven major phenolic compounds identified in all samples. Their content was modified by harvest date and in late harvested apples was increased by controlled atmosphere storage. Antioxidant activity, evaluated by ferric reducing antioxidant power (FRAP), radical 2,2-diphenyl-1-picrylhydrazyl scavenger capacity (DPPH) and TROLOX equivalent antioxidant capacity (TEAC), remained unchanged during the whole storage for both harvest dates. The concentration of sucrose decreased, while glucose increased and fructose remained unchanged during the storage time for both harvest dates. The present results suggest that, under the storage conditions used, nutrients and bioactive compounds of apples were maintained for at least 8 months and phenolic profile was modified by harvest date and storage.