Lotus seed juice has significant potential in the plant-based beverage market owing to its distinctive flavor. However, its sensory quality is significantly influenced by processing and storage conditions. This study examined the effects and underlying mechanisms of fresh squeezing, sterilization, and refrigeration at 4 °C (for 1-6 months) on the aroma profile of lotus seed juice using an electronic nose, gas chromatography-ion mobility spectrometry (GC-IMS), and non-targeted metabolomics. Sterilization processes resulted in vanilla, mint, and ammonia-like flavors due to the accumulation of hexanal, pentanal, and pyrrolidine. One month of refrigeration enhanced fruity and minty flavors, attributed to increased acetone and 6-ethyl acetate-D from fatty acid oxidation and esterification, respectively. However, prolonged refrigeration (six months) introduced undesirable alcoholic and pungent off-flavors caused by slow oxidative degradation (such as 2-propanol and 1-hydroxy-2-propanone). These findings provide valuable insights for improving the preservation methods and quality control strategies for plant-based beverages.