The objective of this study was to determine the effect of various storage conditions (i.e., storage under regular air with temperature control, controlled atmosphere storage and storage after the application of the ethylene blocker (1-MCP)) on the flavor characteristics of Crimson Crisp apples (Malus domesticaBorkh.), a scab-resistant cultivar suitable for organic agriculture. Highly ripe organically-grown apples (starch degradation 9.7) were stored under different conditions and evaluated for physicochemical attributes such as fruit weight, firmness, juiciness, total soluble solids, titratable acidity, pH value and aroma profile. The analysis of primary and secondary aroma compounds was conducted utilizing HS-SPME-GCMS and the results were integrated with sensory evaluation. Crimson Crisp apples stored under controlled atmosphere with (MCP) or without (CA) application of 1-MCP, had a higher overall quality than those stored in air (RA) after a storage period of six months. The results from sensory analysis indicated that storage with temperature control alone was not suitable for preserving the distinct properties such as crispness or juiciness of Crimson Crisp apples. However, a significant increase particularly in secondary aroma compounds in RA-stored apples was found accompanied by structural disorders of the apple tissue. While a significant decline in the volatile fraction of CA and MCP-stored apples was observed, PCA showed close correlation between the CA stored and the fresh apple samples. Furthermore, these results demonstrate that the applied measures which are taken to prolong the storage time of Crimson Crisp apples, significantly impact the biochemical reactions in the fruits which are responsible for formation of flavor. These findings underscore the significance of comprehensive aroma analysis for new agricultural products and emphasize the potential for improved the quality of organic apples through carefully considered harvest and storage regimes.