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Most Brazilian soils have deficiencies of B and Zn, and demand the supply of these nutrients so that production is not hampered. The present study aimed to test the application methodology and doses of B and Zn in perennial soybean seeds. The physical, physiological and nutritional characteristics of the covered seeds and the initial growth of the plants were evaluated in laboratory and greenhouse. Two methodologies were used for the application of micronutrients. In Method 1, the B and Zn doses were added once in the 6th coating layer, followed by a jet of glue, after the first portion of lime + glue. In Method 2, the doses of micronutrient were divided into four equal and individual portions, to be applied to the 3rd, 6th, 9th and 12thlayers followed by a jet of glue. This was added after the first portion of lime + glue. For both the methods, 7 treatments were defined: TR1 - Seeds without coat; TR2 - Coated seeds without micronutrients; TR3 – 50 g of H3BO3 kg-¹ of seeds + 50 g of ZnSO4 kg-¹ of seeds; TR4 – 100 g of H3BO3 kg-¹ of seeds + 50 g of ZnSO4 kg-¹ of seeds; TR5 – 150 g of H3BO3 kg-¹ of seeds + 50 g of ZnSO4 kg-¹ of seeds; TR6 – 150 g of H3BO3 kg-¹ of seeds + 100 g of ZnSO4 kg-¹ of seeds; TR7 – 200 g of H3BO3 kg-¹ of seeds + 100 g of ZnSO4 kg-¹ of seeds. For laboratory tests, a completely randomised design was performed, and randomised blocks were used in greenhouse tests. Methods 1 and 2 increased the B + Zn contents in the seeds by approximately 97 times and 22 times respectively. The micronutrient application methodology in the 6th coat layer promoted greater increases in seed mass and higher levels of B and Zn. Consequently, the plants originated from these seeds had their vigour reduced. Both methods did not significantly influence the initial plant growth.