The objective of this study was to investigate the effects of low-oxygen storage and 1-methylcyclopropene (1-MCP) on disorders and quality of ‘Empire’ apples. For 2 years, ‘Empire’ apples were obtained from commercial orchards during their harvesting period. After cooling overnight at 3 °C, the apples were treated with or without 1-MCP (1 µL·L−1) for 24 hours and subsequently stored in controlled atmosphere (CA) with 2.5 kPa O2 (+2 kPa CO2) or 1.5 kPa O2 (+1.2 kPa CO2) for 8 months at 1.5 and 3 °C for the first and second year, respectively. In the second year, a third group of the ‘Empire’ apples was also held in respiratory quotient (RQ)-based dynamic CA storage (SafePod) that reached 0.6 kPa O2 (+0.5 kPa CO2), and half of these apples were treated with 1-MCP (1 µL·L−1) for 24 hours at 3 °C upon removal after 8 months. All apples were then evaluated for disorders and quality after 1, 7, or 14 days at room temperature (RT, 23 to 24 °C). Substantial external CO2 injury, flesh browning, and core browning (up to 38% incidence) developed in ‘Empire’ stored in 2.5 and 1.5 kPa O2 during both years of study. Storage in 1.5 kPa O2 reduced flesh browning in the first year and core browning during the second year in apples without 1-MCP, as compared to storage in 2.5 kPa O2. 1-MCP-treated apples stored in 2.5 or 1.5 kPa O2 had higher overall incidence of disorders than similar fruit without 1-MCP. In contrast, there was negligible incidence (0% to 1%) of these disorders in ‘Empire’ apples held in 0.6 kPa O2, regardless of 1-MCP treatment upon removal. Storage in 0.6 kPa O2 also resulted in the greatest fruit firmness retention while at RT for 14 days. This regime can provide flexibility to postpone 1-MCP treatment until after storage, to prevent increased susceptibility to disorders during storage, without compromising fruit quality. However, results from the RQ-based dynamic CA with 0.6 kPa O2 were from a single season, and further research is needed to confirm these observations.