Nutrient deficiencies in soil–crop contexts and inappropriate managements are the important reasons for low crop productivity, reduced nutritional quality of agricultural produce and animal/human malnutrition, across the world. The present investigation was carried out to evaluate nutrient deficiencies of sulphur (S) and micronutrients [zinc (Zn), boron (B), iron (Fe), copper (Cu) and manganese (Mn)] in agricultural soils of India for devising effective management strategies to achieve sustainable crop production, improved nutritional quality in crops and better animal/human health. A total of 2,42,827 surface (0–15 cm depth) soil samples were collected from agriculture fields of 615 districts lying in 28 states of India and were analysed for available S and micronutrients concentration. The study was carried out under the aegis of All India Coordinated Research Project on Micro- and Secondary-Nutrients and Pollutant Elements in Soils and Plants. The mean concentrations were 27.0 ± 29.9 mg kg−1 for available S, 1.40 ± 1.60 mg kg−1 for available Zn and 1.40 ± 4.70 mg kg−1 for available B, 31.0 ± 52.2 mg kg−1 for available Fe, 2.30 ± 3.50 mg kg−1 for available Cu and 17.5 ± 21.4 mg kg−1 for available Mn. There were variable and widespread deficiencies of S and micronutrients in different states. The deficiencies (acute deficient + deficient + latent deficiency) of S (58.6% of soils), Zn (51.2% of soils) and B (44.7% of soils) were higher compared to the deficiencies of Fe (19.2% of soils), Cu (11.4% of soils) and Mn (17.4% of soils). Out of 615 districts, > 50% of soils in 101, 131 and 86 districts were deficient in available S, available Zn and available B, respectively. Whereas, > 25% of soils in 83, 5 and 41 districts had deficiencies of available Fe, available Cu and available Mn, respectively. There were occurrences of 2-nutrients deficiencies such S + Zn (9.30% of soils), Zn + B (8.70% of soils), S + B (7.00% of soils) and Zn + Fe (5.80% of soils) to a greater extent compared to the deficiencies of Zn + Mn (3.40% of soils), S + Fe (3.30% of soils), Zn + Cu (2.80% of soils) and Fe + B (2.70% of soils). Relatively lower % of soils were deficient in 3-nutrients (namely S + Zn + B, S + Zn + B and Zn + Fe + B), 4-nutrients (namely Zn + Fe + Cu + Mn) and 5-nutrients (namely Zn + Fe + Cu + Mn + B) simultaneously. The information regarding the distribution of deficiencies of S and micronutrients (both single and multi-nutrients) could be used by various stakeholders for production, supply and application of right kind of fertilizers in different districts, states and agro-ecological regions of India for better crop production, crop nutritional quality, nutrient use efficiency, soil health and for tackling human and animal malnutrition.