In the world, red beetroot is regarded as one of the most important vegetables due to its valuable nutritional features; however, the industrial processing of beetroot produces large amounts of waste, such as skin, which could be a relevant source of bioactive compounds, minerals, fiber, and so on. In this study, the variations in the proximate composition, mineral element amounts, and some antioxidants in the skin and flesh of beetroot genotypes grown in Lithuania were appraised. Proximate compositions (total soluble solids, dry matter, fiber, protein, ash, and total sugars), amounts of some minerals (N, P, Ca, Mg, K, Fe, Zn, Cu, B, and Mn), total phenolics, and total anthocyanins and betalains were determined. The results revealed that proximate composition, minerals, total phenolics, and total anthocyanins and betalains depends on the root part and genotype of the beetroot. All investigated beetroot skin samples have significantly greater amounts of protein, dry matter ash, fiber, total sugars, minerals (except K), total phenolics, and total anthocyanins and betalains than the flesh. ‘Alto F1’ skins had the highest amounts of protein, fiber, ash, Na, Mg, and Zn. ‘Kosak’ skins contained the greatest amounts of dry matter, total sugars, K, P, Ca, Fe, Mn, and total anthocyanins and betalains. It can be concluded that the tested beetroot skins (especially ‘Alto F1’ and ‘Kosak’), due to their valuable nutritional compositions, can be used as a source of natural supplements that can enrich the quality of various food products or be used for the manufacture of functional food.