The objective of this study was to investigate the effects of long-term application of ammoniacal N fertilizer for 43 years on the availability of 10 essential elements (B, N, Mg, K, Ca, Mn, Fe, Ni, Cu, and Zn) and Al in root-zone soils and their supply to 'Jonathan' apple trees. To achieve this objective, we used simultaneous multi-element analysis. To estimate the soil depth from which the apple trees took up these elements, we calculated the ratios of their concentrations in the N fertilized plot (N plot) to those in the no N plot (0 N plot) (N/0N ratio). Long-term N fertilization significantly increased the fruit and leaf N/0N ratios of N and Mn and significantly decreased that of K. These ratios in the fruits and leaves were similar to those in the 20-90 cm soil layer. This result suggests that N, K, and Mn in the fruits and leaves were supplied from the 20-90 cm soil layer. The N/0N ratios of all 11 elements in the fruits and leaves were significantly positively correlated with those in the 20-90 cm soil layer, but not in the 0-20 cm soil layer. Our findings indicate that long-term N fertilization altered the tree nutrition of not only N, but also K and Mn. These changes in the tree nutrition were ascribed to the fertilizer-induced changes in the availability of elements in the subsoils.