Calcium foliar applications are known to effectively enhance peach quality; however, the optimal implementation strategy regarding fruit developmental stages and cultivars remains unclear. In this study, three different moments of fruit Ca applications in peach and nectarine are tested: Early season, Mid-season, and Late season. For this aim, the 44Ca isotope was used as a tracer, enabling the quantification and location of the Ca derived from the foliar fertilizer. Stone, flesh, and skin 44Ca enrichment was separately analyzed at harvest. The results indicate that Ca absorption in the fruits from external CaCl2 applications was influenced by the timing of the application during fruit development, with Late-season applications proving to be the most effective in increasing the Ca content in the fruit, corresponding with a higher fruit size at the application moment. Nevertheless, no differences in the absorption efficiency were found between the three timings of the application. Furthermore, the Ca from the foliar fertilizer in the fruit predominately remained in the flesh, followed by the skin. The Ca derived from the foliar fertilizer reached the stone in all of the experimental situations, but the Early- and Mid-season applications resulted in the highest amount of Ca derived from the fertilizer in this part of the fruit. Interestingly, the peach exhibited a higher Ca absorption efficiency compared to the nectarine, likely due to the presence of trichomes that retain the foliar fertilizer on the fruit surface. In conclusion, the Ca absorption and distribution in peaches depends on the cultivar and timing of the Ca application.