The impact of melatonin (50 µM L−1) applied to Vigna radiata seeds by hydro-priming on phenolic content, L-phenylalanine ammonialyase (PAL) activity, MEL level, antioxidant properties of ethanol extracts as well as electrolyte leakage from chilled and re-warmed Vigna radiata roots of seedlings were examined. Seedlings obtained from non-primed seeds, hydro-primed and hydro-primed with MEL were investigated after 2 days of chilling and 2 days of re-warming. At 25°C, the level of MEL in roots derived from seeds hydro-primed with MEL was 7-fold higher than in roots derived from non-primed seeds. However, the content of MEL significantly decreased in all variants investigated after re-warming, in contrast to PAL activity and phenolic levels, which reached the highest values. The antioxidant capacity of ethanol extracts from chilled and re-warmed roots, determined by ABTS+· assay, was correlated with phenolic content while the reducing ability of these extracts, determined by the FRAP method, correlated with PAL activity. However, both were the highest in rewarmed roots with applied MEL, which was accompanied by a significant decline in electrolyte leakage. Taken together, results may indicate that MEL can play a positive role in plant acclimation to stressful conditions and activation of phenolic pathway by this molecule.