Seed storage reserves and organelles after scarification (chemical, mechanical, control) of bambara groundnut with different seed coat colours (cream, light brown and brown) were examined in relation to germination vigour. Seed storage proteins, oil and sugar content, starch granules and protein bodies, germination vigour index (GVI) and mean germination time (MGT) were measured. There were significant (p < 0.05) effects of seed scarification on protein body diameter, seed oil content and sugar content. Chemical scarification resulted in seeds having larger starch granules, followed by the control and mechanical scarification that resulted in seeds having smaller starch granules. Mechanical scarification had the highest (p > 0.05) protein density, followed by chemical scarification and control seeds that had the lowest protein density. Seeds from the control had the highest oil content, followed by seeds from mechanical scarification and seeds from chemical scarification that had the lowest oil content. Seeds from the control and chemical scarification had larger diameter of protein bodies and sugar content. Seed coat colour significantly (p < 0.05) influenced the area and diameter of protein bodies, starch granule area, seed sugar content. Brown seeds produced larger protein bodies and the highest oil content, while light brown seeds had larger area of starch granules and the highest sugar content. Seed storage reserves had an influence on bambara groundnut germination vigour. While favouring dark coloured seeds such as light brown and brown, bambara groundnut seed users should adapt chemical seed scarification to enhance germination vigour of this crop.