Advances in research and technology in recent years in the field of controlled atmosphere (CA) storage have led to the development of many new protocols that recommend lower oxygen (O2) levels than those historically deemed “safe”. As some of these protocols and technologies have been adopted by commercial CA storage rooms, especially in the apple industry, it is now opportune to review the relationships between O2 levels, respiration, fermentation, and fruit quality retention. Lowering O2 levels during apple storage slows respiration, reduces ethylene biosynthesis, and slows fruit maturation and senescence. In addition, low O2 influences the expression of genes associated with cellular energy consumption. When O2 levels become limiting, aerobic mitochondrial respiration is inhibited and plant tissues engage in the energetically less-efficient fermentation pathway. The accumulation of fermentation-related volatiles may lead to off-flavours and odours. At low levels, or for short durations, fermentation is generally not a problem and may even be commercially beneficial. Plants that are limited in their ability to ferment succumb to low-O2 stress more quickly than those that can readily ferment anaerobically. Increasing market pressure to reduce chemical residues in apple, as well as in all fruits and vegetables, is encouraging researchers, CA system manufacturers and suppliers, and some commercial storage operators to explore alternative methods to improve storage procedures. The future of CA storage may reside in a better understanding of what constitutes the lower O2 limit for metabolism and energy demands, improved product-response sensing capabilities, and the application of more dynamic forms of CA storage technology.