Weed competition can severely reduce soybean (Glycine max (L.) Merr.) yields, particularly in organic systems. An efficient screening and breeding approach is needed to increase breeding progress for weed tolerance. This study sought to (i) establish a system for direct selection of competitive genotypes, (ii) evaluate genotypic differences in weed tolerance among six early‐maturing genotypes and (iii) assess the contribution of selected morphological traits to weed tolerance. A direct selection system providing two different levels of weed competition through all development stages of a soybean crop was developed, using mixtures of selected crop species as sown competitors. Two resulting mixtures induced intermediate (<30%) and strong (>50%) yield reduction, respectively. This selection system can be applied in screening and breeding programmes to facilitate breeding for weed tolerance. No significant difference in weed tolerance was detected between six soybean genotypes of maturity groups 000 to 00. Morphological traits that might influence competitive ability, for example light absorption, leaf area and lateral shoots, were assessed, and their potential for indirect selection for weed tolerance is discussed.