This study aimed at understanding the uptake pathway of combined copper, zinc, and molybdenum applied to soybean (Glycine max (L.) Merrill) and maize (Zea mays (L.) seeds and their effect on seedling development. Two doses—2 and 4 mL kg⁻¹ seeds—of a mixed copper, zinc, and molybdenum formulation were applied on both seed species, and process efficiency, i.e., how much of the applied solutions were transferred to the seeds, was determined. The spatial distribution of these nutrients was examined through microprobe X-ray fluorescence spectroscopy, and the effects on seed germination and seedling’s root and shoot development were recorded. Besides, the fraction of applied nutrients transferred from the seeds up to the seedlings tissues and the efficiency of the coating process were quantified. The results showed that seed treatments presented an overall efficiency of 70%. Most of the nutrients applied remained attached to the seed surface, i.e., seed coat or pericarp tissues in both species, being transferred to the soil afterwards. Only a tiny fraction of zinc, copper, and molybdenum was found in root and shoot tissues germinated from the coated seeds. The treatments did not impair seed germination or affected the content of the other mineral elements in the root and shoot tissues, although it had promoted a slight increase on maize’s root tissue length and dry mass. These results bring to light that the current seed treatment transfers part of the nutrients directly to the early developing seedling, while the remaining is precisely deposited in the soil volume where the root system will develop.