Aims Because plant roots serve mainly as organs for the uptake of water and nutrients, we aimed to test whether the development of seedling roots is influenced by the two principal nutrient sources—the substrate and the pool stored in the seed itself. Methods Using seven Fabaceae species that differ in seed mass, we observed their early root system development under four levels of nutrient availability. Transparent-wall rhizoboxes allowed us to track root development and to score root system structure (length and number of roots), size (depth and width of root system) and shape (relative depth and width of root system). Results Seedling root system development depended on both the amount of nutrients contained in the substrate and on the seed mass of the species. Compared to an average seedling, effects of these two nutrient pools were (i) opposite and (ii) did not fully overlap. Small-seeded species developed wider root systems that branched earlier than large-seeded species. Increased availability of nutrients in the substrate led to proliferation of lateral roots, without any substantial impacts on the shape of root system or beginning of branching. Conclusions The source of the nutrients affected the way they were used throughout early root system development, leading to different structures and dynamics. This may be one of the mechanistic links connecting seed mass and the realized niche of the species.