This chapter highlights advances in controlled atmosphere (CA) storage science of horticultural crops (mainly apples and pears) over the last two decade, emphasizing the connection between technical/managerial aspects of the CA regime and retention of product quality during and after the storage period. The chapter particularly focuses on: initial low O2 stress (ILOS); delayed CA storage; anti-ethylene compounds (e.g. 1-MCP); dynamic controlled atmosphere (DCA) systems based on chlorophyll fluorescence (CF), ethanol detection and respiratory quotient (RQ) determination for identifying the lower oxygen limit (LOL); and strategies for reducing the electrical energy demands of the storage room. The chapter concludes with a reflection upon likely future advancements in CA storage science over the next 10-20 years, including: refining and broadening DCA system and 1-MCP application (singly and together), more metabolomic research to understand the biochemical and molecular effects of hypoxic stress, and new protocols for reducing storage room-related electricity consumption.