The impacts of integrated soil fertility management (ISFM) in conservation agriculture need short-term evaluation before continuation of its long-term practice. A split-split plot experiment with tillage (minimum tillage, MT vs. conventional tillage, CT) as the main plot, residue (20% residue, R vs. no residue as a control, NR) as the sub-plot, and compost (Trichocompost, LC; bio-slurry, BS; and recommended fertilization, RD) as the sub-sub plot treatment was conducted for two consecutive years. Composite soils were collected after harvesting the sixth crop of an annual mustard-rice-rice rotation to analyze for nutrient distribution and soil structural stability. The LC increased rice equivalent yield by 2% over RD and 4% over BS, and nitrogen (N) uptake by 11% over RD and 10% over BS. Likewise, LC had higher soil organic carbon (SOC), N, and available sulphur (S) than BS and RD. Conversion of CT to MT reduced rice equivalent yield by 11%, N uptake by 26%, and N-use efficiency by 28%. Conversely, soil structural stability and elemental quality was greater in MT than in CT, indicating the potential of MT to sequester C, N, P, and S in soil aggregates. Residue management increased rice yield in the second year by 4% and corresponding N uptake by 8%. While MT reduced the yield, our results suggest that ISFM with Trichocompost and residue retention under MT improves soil fertility and physical stability to sustain crop productivity.