The influence of nickel (Ni) and/or selenium (Se) on phospholipid composition was studied in shoots and roots of wheat seedlings. Phospholipid differences between samples were analysed using liquid chromatography/electrospray ionization–MS coupled. A total of 39 lipid species were identified. Individual phospholipids were then quantified using a multiple reaction monitoring method. In the roots, Ni toxicity was associated with an elevated level of phosphatidic acid species. In the shoots, the phosphatidylcholine/phosphatidylethanolamine ratio was about fivefold higher than in roots and decreased in Ni-treated samples. Additionally, the concentrations of phospholipid species containing C 18:3 fatty acid were reduced. Lipidome data were then analyzed using principal component analysis, which confirmed the compositional changes in phospholipids in response to Ni and Ni + Se. In contrast, the phospholipid profiles of wheat seedlings exposed to Se alone showed more similarities with the control. Together, our results suggested that the presence of Se, despite a considerable improvement of growth of Ni-treated wheat, did not counterbalance negative effect of Ni on the phospholipid composition in wheat roots and shoots.