The need to focus on traditional crops for food security has been realized across the globe. ‘Bhat’ is an indigenous soybean variety from the Indian Himalayan Region that has been neglected in recent times due to changing agricultural choices. The present study was conducted on 52 indigenous soybean accessions collected from different villages of Uttarakhand, a hilly state in Northern India, to determine the concentrations of various macro- and microelements in the crop. The analysis used the HHXRF (handheld X-ray fluorescence) spectroscopic technique and atomic absorption spectroscopy (AAS). The findings reveal that the ‘bhat’ is an extremely nutrient-rich crop with calcium being the most significant macronutrient (highest concentration of 27,300 ppm), followed by phosphorus, potassium, and sulphur found in the bhat seeds. The study suggests that samples from Pauri Garhwal (Gwad Khirsu, Bironkhal, Sripur), Tehri (PratapNagar, Singoli), Chamoli (Paini, and Agastyamuni) villages were rich in all the major macronutrients. Among the micronutrients, silicon was found to be the most dominant with the highest concentration of 1920 ppm. This was followed by the dominance of iron, zinc, and manganese in descending order of abundance. Tipri, Chandola Rai Goonth, Chopdiun, and Paini villages were found to have the highest concentrations of microelements. The statistical data analysis confirms that seed samples from different regions are significantly similar in terms of nutrient concentrations, except for Si and Fe, thereby indicating that ‘bhat’ from any of the villages is equally good for consumption. However, seed samples from certain regions were found to be contaminated with heavy metals, indicating soil pollution, which demands attention towards current agricultural practices. The findings show that the crop is an exceptional source of essential and quasi-essential elements and should be promoted to benefit the hill populations.