On a worldwide scale, A. cepa is among the most commonly consumed vegetables. In Europe, the leading onion producers are Russia, the Netherlands, Spain, Poland and Germany. In this study, the bioaccumulation of heavy metals (Cr, Cu, Zn, Ni, Fe, Mn, Co, Sr, Cd and Pb) by Allium cepa L. plants was followed under hydroponic conditions. The heavy metals were applied at six concentrations (0, 25, 50, 100, 200 and 400 mg L−1) over three weeks. The quantitative analysis of selected heavy metals in plant tissues (bulbs, roots and assimilation leaves) was performed using atomic absorption spectrometry with flame atomization (F-AAS). The accumulation of metal ions was strongly dependent on their concentrations in the solution and the analyzed parts of plants. The highest accumulation of metal ions was confirmed for the roots and ranged from 8.48 to 5912.34 µg g−1 DW (dry weight). All parts of A. cepa were characterized by the high accumulation of Mn2+. The lowest accumulation was confirmed for Co2+ in the roots, Pb2+ in the assimilation leaves and Cu2+ in the bulbs of onion. Moreover, the study showed that the highest concentrations of heavy metals decreased the growth of bulbs and even caused them to die off. In contrast, lower concentrations of some elements stimulated plant development.