Essential trace metals are well known for their environmental toxicity and for being part of complex bio-chemical cycles. Their role as critical micronutrients, delivering vital health benefits, is less widely discussed and understood, holding back strategies for combatting malnutrition. Crops grown on many Indian soils suffer from deficiencies in essential metals, notably iron (Fe), zinc (Zn), and molybdenum (Mo). The list of deficient metals will likely grow due to increasing future crop demand. Geostatistical analysis of soils and farmyard manure (FYM), the predominant fertiliser, implies that residual oxide minerals carry high concentrations of the essential trace metals Fe, Zn, copper (Cu), chromium (Cr), nickel (Ni), cobalt (Co), manganese (Mn) not only in soil but also in FYM (especially Fe, Cr, Cu, Co and Ni). A geochemical survey across a road traverse of 600 km, encompassing an area of c. 15,000 km2, was conducted in Central India to evaluate reported essential metal deficiency in key agricultural topsoils. Importantly, our evaluation of the element cycling in this system reveals that despite high bulk concentrations, some key metals remain bio-unavailable. In effect, the existence of refractory (weathering-resistant) oxides is likely a significant factor for deficiency symptoms in the soil–plant-fertiliser cycle. Further, mass balance calculations of the bioavailable pool of metals imply that only Fe and Mn are present in sufficient quantities to combat deficiency problems. Notwithstanding this limitation of FYM, its high organic carbon content, as well as its importance for Zn, Cu and Fe, validates its traditional use to maintain the fertility and physical condition of Indian topsoils.