Seed coat integrity (porosity, colour and thickness) and structure (hilum, strophiole and micropyle) explain, predict and even allow genotypes resistant to pre-harvest sprouting (PHS) and field weathering under certain environmental conditions. This study examined how morphological and biochemical seed coat characteristics and their role in mitigating PHS in 96 soybean genotypes. All traits showed significant genetic variation, with broad-sense heritability ranging from 0.336 to 0.611. The principal component analysis (PCA) revealed that the first two components explained 62.50 % of total variation. Seed coat proportion correlated strongly with peroxidase activity (POD) (r = 0.511) and negatively with and water absorption capacity (WAC) (r = -0.533). Seeds had black (4 genotypes) and yellow (92 genotypes) seed coats and grey (5 genotypes) and brown (91 genotypes) seed hilums. Physical and biochemical characterisation varied in 96 genotypes, including Birsa Soya 1, Kalitur, Pune 14, Pune 30 (lack colour) and MAUS 61-2 (yellow colour) which were found resistant to field weathering due to hard seed coat (HSC) and seed colour. Black and brown testa genotypes are resistant to field weathering because they have the highest percentage proportion of seed coat, seed thickness (ST) and minimum seed coat permeability than yellow genotypes, which have a delicate seed coat, minimum mechanical strength and maximum seed coat permeability. These findings provide useful selection criteria for breeding soybean cultivars with improved resistance to PHS under humid tropical environments.