Many of today’s innovative materials used to carry trace elements (TEs) are derived from chelates. Most of the materials used for this purpose have been produced on the basis of EDTA, which is not considered to be environmentally friendly due to its high persistence. Research is therefore being carried out to produce materials that do not pose an environmental risk. Therefore, a study was carried out to determine the effects of newly developed innovative materials with embedded biodegradable and environmentally safe chelates (IDHA—iminodisuccinic acid—and N-butyl-D-gluconamide ligands) containing copper, molybdenum and iron on the yield, biometric characteristics and chemical composition of soybean and selected soil properties. It is difficult to find publications on their effects in soybean cultivation. The greatest increase in soybean leaf greenness index (SPAD) was found after the addition of pure Salmag® (Sal.®). The effect of the chelates on the SPAD index was lower, with Sal.® + Fe chelate having the greatest effect during the vegetative development stage and Cu chelate having the greatest effect during the flowering stage. Sal.® + Cu, especially with Fe, accelerated pod and seed ripening in the last vegetative stage of soybean. Sal.® + Cu had the most favourable impact on plant height, pure Sal.® on the pod number per plant, Sal.® + Fe on the seed number per pod, Sal.® with Mo and Fe chelates on soybean seed yield, and pure Sal.® on fresh weight remaining above-ground part yield, while pure Sal.® and Sal.® + Fe had the most favourable impact on dry weight aerial yield. The fertiliser materials (especially Sal.® + Cu) generally increased the N content of the tested soybean organs and the Cu content of the other above-ground soybean parts (especially those containing chelates) and had an antagonistic effect on the Mg content of the soybean above-ground parts. Sal.® + Cu also had a negative effect on the Fe content of other above-ground soybean parts. Sal.® + Fe had a positive impact on the iron content, and Sal.® + Mo had a positive impact on the molybdenum content of soybean. The applied fertilisers had little effect on the contents of Cu, Mo and Fe in the soil. There was only a significant increase in the Cu content of the soil after the addition of Sal.® + Cu and a significantly smaller increase under the influence of Sal.® without chelates, as well as an increase in the Mo content of the soil with Sal.®. The present study confirms the beneficial impact of the novel materials with chelates. It has been demonstrated that the presence of materials containing Mo and, in particular, Cu has a considerable effect on the yield and quality characteristics of soybeans.