Elderberry growth phases represent an irreversible process involving a series of biochemical changes that have an extremely important impact on nutritional characteristics. The aim was to assess the impact of genotype and maturity stage on phenolic compounds, antioxidant capacity and mineral profile in Sambucus plants harvested during different growth phases, from green elder flower buds to purple-black elderberries, including pollen, peduncles and seeds. Growth phases proved to have a greater influence compared to varieties. The green buds and flowers of both varieties had a high concentration of quercetin 3-rutinoside, also termed the key compound of the study. It was found that antioxidant activity varied in the following order: blooming elder flower pollen > white elder flower buds > blooming elder flowers. Based on these findings, several novel food ingredients and supplements could be obtained in order to develop innovative health-promoting products.