Dwarf elder (Sambucus ebulus L.) berries are rich in health-promoting phytochemicals such as polyphenols and anthocyanins, and display a significant antioxidant activity. They are also rich in two lectins (ebulin f and SELfd) that share amino acid sequence homology with the elderberry allergen Sam n1 present in Sambucus nigra pollen and fruits. Ebulin f displays toxicity by oral ingestion. This study was aimed at eliminating the toxicity of these lectins whilst having little or no effect on the antioxidant properties of dwarf elder berries. We thus investigated the potential effects of incubation in a boiling water bath of extracts from several parts of the plant on total polyphenol content, antioxidant activity, total anthocyanins, cyanidin-3-glycoside content, and the sensitivity of purified dwarf elder fruit lectins to a simulated gastric fluid. The study shows that five minutes of said heat treatment fully sensitized both lectins to pepsin digestion, whilst minimally reducing phenol and antioxidant as well as free radical scavenging activities to below 13%. It proved possible to eliminate the potential risks derived from the presence of lectins in dwarf elder juices without any significant reduction in the content of the antioxidant compounds. Dwarf elder berries may thus be a valuable nutritional source.