The impact of low-oxygen (2 kPa) controlled atmosphere storage on the recovery of aroma biosynthesis in ‘Golden Delicious’ (GD) apple tissues during their subsequent shelf life was investigated. The results showed that the highest ester content was found in skin tissue, followed by Flesh 2 and Flesh 1. The 2 kPa O₂ storage of GD apples resulted in a decrease in the emission of volatile esters and alcohols, but an increase in aldehyde emission. Notably, compared with skin tissue, the flesh tissue of 2 kPa O₂-stored GD apples had a relatively high recovery capacity of ester biosynthesis but a low recovery capacity of alcohol synthesis for its shelf life. The impact was associated with increased levels in the MdLOX1a and MdAATs (MdAAT1 and MdAAT2) transcripts, as well as a decreased level in the MdHPL transcript in the flesh tissue. In addition, a complex regulatory network of ethylene on fruit aroma biosynthesis in response to low-oxygen conditions was also indicated. Collectively, there was a tissue-specific recovery capability of aroma biosynthesis in GD apples after low-oxygen storage.