The present study was carried out under two on-going field experiments at research farm, Department of Soil Science, Punjab Agricultural University, Ludhiana in split plot design with three replications. The soil of both experimental fields was loamy sand in texture, taxonomically classified as Typic Ustrochrept. The first experiment comprised of twelve treatment combinations among which the main plots consisted of four rice establishment methods viz. direct seeded rice under zero tillage (DSR-ZT), conventional tillage (DSR-CT), reduced tillage (DSR-RT) and puddled transplanted rice (PTR) and three subplots in wheat viz. conventional tillage (CTW-R), zero tillage without rice straw (ZTW-R) and zero till with rice straw (ZTW+R). In this study, soil samples were analyzed for basic chemical indices of soil quality. The DTPA-extractable micronutrient cations (Zn, Fe, Mn and Cu) and their different chemical fractions were analyzed using atomic absorption spectrophotometer (Varion AAS-FS Model). The ZTW+R showed marked increase in concentration of DTPA-extractable Zn, Fe, Mn and Cu and their transformation from occluded fractions towards bio-available forms. Residual fraction of all the micronutrient cations was found to be the most dominant fraction and water soluble + exchangeable fraction was found to be least dominant in soil. Organically bound fraction of all the micronutrient cations studied was found to be most important fraction contributing towards micronutrient uptake by both rice and wheat crops. The ZTW+R produced significantly higher wheat grain yield than ZTW-R. Moreover, rice grain yield under PTR and DSR-RT was comparable but significantly higher than DSR-CT and DSR-ZT. The second experiment consisted of twelve treatment combinations among which the four main plots comprised of puddled transplanted rice with no wheat straw retained (PTRW0), puddled transplanted rice with 25% anchored wheat straw retained (PTRW25), PTRW0 + GM and PTRW25 + GM. Similarly, three subplot treatments included conventional tillage wheat without rice residue (CTWR0) zero tillage wheat without rice residue (ZTWR0) and ZTW with 100% rice residue retained as mulch (ZTWR100) in subsequent wheat crop. The results of the study revealed that soil pH decreased however, SOC and availability of DTPA-extractable micronutrients increased with crop residue retention and GM incorporation in soil. The DTPA-extractable Zn, Cu, Fe and Mn showed sharp decrease from 0-7.5 cm to 7.5-15 cm soil depth and afterwards the decrease was gradual with further increase in soil depth. The transformation of Zn, Cu, Fe and Mn was found higher under PTRW25 + GM treatment from occluded (AFeOx and CFeOx) fractions to mobile (WSEX) ones. Highest productivity and Zn, Cu, Fe and Mn uptake by grain and straw of rice and wheat were also recorded under PTRW25 + GM treatment. In nutshell, green manure incorporation and crop residue retention over the soil surface substantially increased the crop productivity and availability of Zn, Fe, Mn and Cu in soil.