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The quality of seeds produced is the result of the management practices used and environmental conditions during growing. The aim of this study was to evaluate the physiological potential and the health of soybean seeds produced in an organic and conventional system. The genotypes UEL 110 and 122 and BRS 257 and 284 were tested in organic and conventional systems in a randomized block design. The following characteristics were evaluated: moisture content; thousand seed weight (TSW); germination (G) and first count of germination (FCG); tetrazolium (TZ); classification, length, and dry matter of seedlings; and seed health. Analysis of variance was performed separately for the management systems, followed by combined analysis. When significant, the Tukey test (p<0.05) was applied. Multivariate analysis was performed using R software. There was not significance between genotypes and management systems. The conventional management system performed positively for the characteristics TSW, G, TZ, FCG, classification, and length and dry matter of seedling roots, as well as for plant health. The UEL genotypes obtained higher TSW; UEL 110, lower germination; and BRS 257, a smaller number of ungerminated seeds and higher infestation by Cladosporium spp. The seeds produced under the organic system have greater weight and lower infestation by contaminants, whereas the conventional system produces seeds of better physiological quality and lower contamination by Phomopsis and bacteria. The genotype BRS 257 may have seeds multiplied in the organic and conventional management systems. [ABSTRACT FROM AUTHOR]