A soilless culture and completely randomised two-factorial experiment was carried out to investigate the effect of nitrogen (N), phosphorus (P) and potassium (K) deficiencies on macronutrient uptake and to determine some characteristics of Prunus dulcis L. (bitter almond: BA) and Prunus scoparia L. (Alook: AL) seedlings. Seedlings in pots containing perlite were irrigated with half-strength, N-, P- and K-free Hoagland solutions for 12 wk. Results showed that N deficiency decreased the N and Ca levels and increased the K concentration in the shoots of both rootstocks. Phosphorus deficiency decreased N and P concentrations of both seedlings, as well as the Ca and Mg concentrations of BA seedlings. Potassium deficiency decreased the K concentration of the BA seedlings and decreased N, K and Ca concentrations of the AL seedlings. In the BA seedlings, only the fresh weight of the shoot decreased under the P deficiency condition; the other morphological traits of shoots in this genotype and none of the traits in the AL seedlings were affected by P deficiency. Furthermore, both the rootstocks can maintain their optimal growth even at very low concentration of K; this shows that both rootstocks consume K in a luxurious way. Under nutrient-deficient conditions, the AL seedling has greater ability to maintain the N concentration or uptake it more than the BA seedling. The N P and K deficiency conditions disturbed the electron transfer cycle of photosystem II in the AL leaves and caused a response. Most root traits of the AL seedling were not changed under nutrient deficiency, and this indicates a high tolerance of the AL roots compared to the BA roots or lower demand in this genotype for these elements. The characteristics of P. scoparia seedlings were less affected by the deficiency of these three elements, and therefore, P. scoparia rootstock is preferred to BA for weak and non-fertile soils.