BACKGROUNDLemon juice vesicles are distinguished by their unique and abundant volatile flavor compounds, which can undergo complex changes during drying. In this study, integrated freeze drying (IFD), conventional freeze drying (CFD), and hot‐air drying (AD) were used to dry lemon juice vesicles to investigate the changes in, and correlations among volatile compounds, fatty acids, and key enzyme activity during the drying process.RESULTSTwenty‐two volatile compounds were detected during the drying processes. Compared with fresh samples, seven compounds were lost in the dried samples after IFD, seven after CFS, and six after AD, and the loss rates of the total content of volatile compounds in the dried samples were 82.73% in CFD, more than 71.22% in IFD, and more than 28.78% in AD. In total, 1.015 mg/g of seven fatty acids were detected in the fresh samples; the content loss rates of total fatty acids after drying were 67.68% in AD, more than 53.00% in CFD, and more than 36.95% in IFD, respectively. During the three drying processes, IFD retained relatively higher enzyme activity in the samples.CONCLUSIONMany positive and negative correlations (P < 0.05) were observed among the key enzyme effects, fatty acids, and volatile compounds, showing close associations. The current work provides information that is important for the selection of suitable drying techniques for lemon juice vesicles and suggests how to control their flavor during the drying process. © 2023 Society of Chemical Industry.