Rice productivity is stagnant or declining due to imbalanced nutrition, including deficiency of sulphur. In India about 44% soils (out of total cultivated land) is sulphur deficient. Various sources of Sulphur fertilizers are available, but gypsum and phosphogypsum can be better options for the farmers. The main aim of this study was to improve the soil fertility, soil microbial properties and rice yields with application of sulphur. The combination of two sulphur sources (gypsum & phosphogypsum) at two levels ie, 30 and 60 kg ha-1 and control (no S) were applied to rice crop and three levels of sulphur (elemental sulphur) ie, 0, 15 and 30 kg S ha-1 were applied to succeeding wheat grown under rice-wheat cropping system. Microbial biomass carbon and microbial activities in terms of Fluorescein Diacetate (FDA) hydrolysis, Dehydrogenase and Arylsulphatase activity were estimated in different treatments by standard procedures. Organic carbon, N, P, K and S were estimated for residual fertility after harvest of rice crop. Rice grain yield was recorded at 14% moisture content. Direct and residual effect of sulphur application increased the wheat grain and straw yield. Sulphur application increased 8.2 to 12.8%(microbial biomass carbon), 16.9 to 32.3%(arylsulphatase activity) and 8.7 to 11.2%(rice grain yield). Available N and P in soil were observed higher in control (no sulphur) than the other sulphur treatments. However, sulphur status after two years of cropping system was improved by 6.4, 12.7, 5.2 and 9.7% with sulphur application through gypsum@ 30 and 60 kg S ha-1; phosphogypsum@ 30 and 60 kg S ha-1, respectively. Sulphur is also essential as microbial-S for the micro-organism. Hence, Sulphur application increased the microbial biomass carbon and arylsulphatase activity. Application of sulphur through gypsum or phosphogypsumin soil improved the soil microbial properties and sulphur availability. Application of sulphur@ 30 kg ha-1 through gypsum can increase the rice yield by 10% over control (no sulphur).