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Imbalanced fertilizer use with intensive cropping has threatened the sustainability of agroecosystems, especially on acid soils. An understanding of the long‐term effects of fertilizers and amendments on soil health is essential for sustaining high crop yields. The effects of application of fertilizers, and amendments for 46 years on soil properties and maize yield in an acid Alfisol were investigated in this study. Ten fertilizer treatments comprising different amounts of NPK fertilizers, farmyard manure (FYM) and lime, and one control, were replicated three times in a randomized block design. At 0–15 cm soil depth, bulk density was least (1.20 t/m3), porosity (49.8%) and water holding capacity (61.7%) were greatest in 100% NPK + FYM, corresponding to the largest organic carbon content (13.93 g/kg). Microbial biomass C and dehydrogenase activity in 100% NPK + FYM were 42% and 13.7% greater than 100% NPK, respectively. Available nutrients were significantly more with 100% NPK + FYM and 100% NPK + lime than control and other fertilizer treatments. At 15–30 cm depth, the effect of various treatments was comparable to the surface layer. Grain yield declined by 55% and 53% in 100% NPK(‐S) and 100% NP, respectively, compared with 100% NPK, whereas 100% N as urea alone eventually led to crop failure. Soil porosity recorded the greatest positive correlation (r = .933**), whereas bulk density recorded a negative significant correlation (r = −.942**) with grain yield. The results suggest that integrated use of FYM/lime with chemical fertilizers is a sustainable practice in terms of crop yield and soil health, whereas continuous application of urea alone is detrimental to the soil health.

A study was undertaken to identify suitable indicators of soil quality from a long-term fertilizer experiment conducted since 1972, which was laid out in a randomized block design with eleven treatments replicated three times. Surface (0-0.15 m) soil samples were collected after harvest of wheat crop during 2010-11 and were analyzed for physical, chemical, and biological properties. Sustainable yield index (SYI) was calculated based on long-term yield data. Highest and lowest overall SYI values were found in balanced fertilization along with manures and urea-only treatments, respectively. Saturated hydraulic conductivity, pH, labile carbon, available phosphorus (P) and potassium (K), pentetate zinc trisodium (DTPA Zn), and nitrogen mineralization were most important minimum dataset (MDS) indicators. The greatest soil quality index (SQI) value was found in balanced fertilization along with manures followed by balanced fertilization along with lime; and the urea-only treatment was the lowest. Balanced fertilization along with manures showed positive change in soil quality and maintained sustainability of productivity.