Synthetic vitamin preparations have grown in popularity to combat health risks associated with an imbalanced diet, poor exercise and stress. In terms of bioavailability and diversity, they lack behind vitamins naturally occurring in plants. Solutions to obtain plant-derived vitamins at a larger scale are highly desirable. B vitamins act as precursors of enzymatic cofactors, thereby regulating important metabolic processes both in animals and plants. Because during plant germination, the vitamin content and micronutrient availability increase, sprouts are generally considered a healthier food as compared to dry grains. Germination only occurs if a plant′s antioxidant machinery is sufficiently activated to cope with oxidative stress. Seeds of quinoa, an edible gluten-free plant naturally rich in minerals, germinate readily in a solution containing the eight B vitamins. We studied biochemical changes during quinoa germination, with a focus on nutritionally relevant characteristics. The results are considered from a nutritional and plant physiological perspective. Germination of quinoa in vitamin-rich medium is a promising strategy to enhance the nutritional value of this matrix. Additional health-beneficial effects indirectly resulting from the vitamin treatment include elevated levels of the multi-functional amino acid proline and a higher antioxidant capacity. Plant biomolecules can be better protected from oxidative damage in vivo.