Understanding the effects of long-term manuring and fertilisation is vital for sustaining soil quality in continuous cropping system particularly in low-fertile Alfisols for developing suitable soil management practices. The research evaluated the impact of long-term manuring and fertilisation on soil quality index (SQI) under finger millet-maize system in Alfisols at the University of Agricultural Sciences, Bengaluru during 2020–22 using a LTFE experiment since 1986. The experiment consists of 11 treatments viz., 50 % nitrogen, phosphorus and potassium (NPK), 100 % NPK, 150 % NPK, 100 % NPK + hand weeding, 100 % NPK + lime, 100 % NP, 100 % N, 100 % NPK + farmyard manure (FYM), 100 % NPK (-S), 100 % NPK + FYM + lime and control in a randomised block design with 3 replications. Soils (Typic Kandic Paleustalfs) were sampled at 0–15 cm after harvest of maize and analysed for various soil indicators. Application of FYM and lime with recommended NPK improved soil quality (e.g., organic carbon, dehydrogenase activity), while unfertilised or imbalanced treatments (N or NP) showed decline. The SQI ranged from 0.64 to 0.99 in surface soils, with organic carbon and pH as key contributors to soil quality. The NPK + FYM + lime treatment showed higher carbon sequestration rate from the initial compared to alone fertiliser application. Integrated application of FYM, lime and recommended NPK significantly improved soil quality, while imbalanced fertilisation led to soil degradation in the long-term finger millet-maize system on Alfisols.