Particle‐induced X‐ray emission was used to investigate mineral accumulation during different developmental stages of direct organogenesis from cotyledon explants of Blepharispermum subsessile beginning from shoot bud initiation and formation to in vitro regenerated roots. Mineral uptake and accumulation appeared selective and varied between different stages of shoot bud initiation and formation (Stage 1), proliferation of leafy shoots (Stage 2), and in vitro regenerated roots (Stage 3). The concentrations of 2 macro elements, K and Ca, were found in higher quantity during proliferation of shoot buds to leafy shoots stage suggesting their role in cell division, bud formation, and multiplication of the plant. Most of the micronutrients such as Mn, Fe, Ni, Cu, and Zn were found to be accumulated in higher quantities in in vitro regenerated roots, as they provide the plant with a larger surface area and hence a greater potential for mineral uptake. The results of particle‐induced X‐ray emission test suggest that the information on the accumulation of elements during developmental stages in vitro could be useful for formulating a media for the induction of high‐frequency regeneration of in this important endangered medicinal plant species for its ex situ conservation.