Mung bean (Vigna radiata (L.) Wilczek) sprouts are popular over the world because of their taste, nutritional value, well-balanced biochemical composition, and other properties beneficial for human health. Germination conditions affect the composition of metabolites in mung bean sprouts, so a detailed study into its variability is required. This article presents the results of a comparison of the metabolite composition in the leaves of mung bean sprouts germinated first in the dark (DS) and then in the light (LS). Gas chromatography with mass spectrometry (GC–MS) made it possible to identify more than 100 compounds representing various groups of phytochemicals. Alcohols, amino acids, and saccharides predominated in the total amount of compounds. The analysis of metabolomic profiles exposed a fairly high intra- and intervarietal variability in the metabolite content. DS and LS differed in the qualitative and quantitative content of the identified compounds. The intravarietal variability was more pronounced in DS than in LS. DS demonstrated higher levels of saccharides, fatty acids, acylglycerols, and phenolic compounds, while amino acids were higher in LS. Changes were recorded in the quantitative content of metabolites participating in the response of plants to stressors—ornithine, proline, GABA, inositol derivatives, etc. The changes were probably induced by the stress experienced by the sprouts when they were transferred from shade to light. The analysis of variance and principal factor analysis showed the statistically significant effect of germination conditions on the content of individual compounds in leaves. The identified features of metabolite variability in mung bean genotypes grown under different conditions will contribute to more accurate selection of an illumination pattern to obtain sprouts with desirable biochemical compositions for use in various diets and products with high nutritional value.