Takuan‐zuke is a traditional Japanese fermented pickle, prepared by dehydration of radish root (daikon) by salt‐pressing or sun‐drying followed by aging with salt. We previously reported that alanine, proline, and γ‐aminobutyric acid (GABA) accumulate during daikon dehydration, whereas the level of glutamic acid, their precursor, decreases. We have also reported that dehydration and salt‐aging markedly influence the dynamics of free amino acids. In this study, we quantitatively analyzed free amino acid levels, enzyme activity, and gene expression to characterize takuan‐zuke amino acid metabolism. Enzyme activities related to alanine, proline, GABA, and glutamic acid metabolism were sustained during dehydration. Moreover, genes encoding alanine, proline, and GABA synthases (ALT1, P5CS1, and GAD4) were significantly upregulated during dehydration. These effects may represent cellular stress responses to the dehydration process. The biological response of daikon contributes to the healthy functional aspects that characterize takuan‐zuke. These findings could guide the selection of suitable vegetable varieties to produce pickled vegetables with health‐promoting properties.Practical ApplicationThe fermented pickle takuan‐zuke, prepared by dehydration of radish root (daikon), accumulates amino acids, such as alanine, proline, and GABA, during preparation that provide taste and health benefits. In this study, the aforementioned amino acids were found to accumulate because of the stress response of daikon during the dehydration process and not because of the action of microorganisms during fermentation. Takuan‐zuke processing is a method for improving the nutrition of daikon.