Zinc (Zn) is a micronutrient considered essential to plants which can be supplied through seed treatment. The treatment of soybean [Glycine max (L.) Merr.] seeds with Zn, however, is still not well known as regards the uptake and mobilization dynamics of the nutrient during the germination process. This study aimed to evaluate the uptake and distribution dynamics of Zn applied to soybean seeds at two levels of vigor during germination using X-ray micro-fluorescence spectroscopy (µ-XRF). Zinc treatments corresponded to 0, 2, 4 and 8 g of Zn per kg of seeds. High and low vigor seeds that had been treated were located appropriately so as to promote germination. Zn intensity measurements with µ-XRF were taken in different parts ("regions") of the seeds (seed coat, cotyledon, and embryonic axis) after 8, 16 and 24 h of imbibition and seedlings (primary root, hypocotyl, plumule, cotyledon, and seed coat) after 48, 72 and 96 h of germination. High vigor seeds showed higher Zn intensity in the embryonic axis in the first 16 h, while low vigor seeds showed higher intensity after 24 h. After 48, 72 and 96 h of germination low vigor seedlings showed higher Zn intensity than high vigor seedlings in the primary root. It was concluded that µ-XRF is an efficient technique for identifying variances in the dynamics of Zn uptake and mobilization during the germination of soybean seeds with different vigor levels.