The study was carried out in designed pots—rhizoboxes. Root systems were evaluated using computer scanning to determine total length, root area, and root diameter. The study showed a favorable effect of deep placement of fertilizers on total yield, increasing biomass yield by 7–17% relative to surface fertilization. The largest biomass increase under the influence of deep fertilization was obtained in the case of tuber yield, in which a yield increase of 18–34% was obtained. Higher yields of potato tubers were obtained under depth fertilization compared to surface application of fertilizers. Under the influence of deep fertilization at a depth of 20 cm, the uptake of nitrogen and phosphorus by potato biomass increased by 20–21%. Increased depth of fertilization increased the proportion of nitrogen accumulated in the tubers, while in the case of phosphorus, no effect of depth on P distribution was shown. An analysis of root system parameters showed a positive effect on increases in length and total root area under deep fertilization of potato plants. Based on the study, it was found that the distribution of dry matter, nutrients, and potato root development parameters were most optimal when fertilizer granules were applied at a depth of 20 cm.