A 2-year field study was conducted to evaluate the effect of two organics, farmyard manure and vermicompost, each at three rates (0, 5, 10 t ha−1 and 0, 1, 2 t ha−1, respectively), along with two levels of mineral fertilizer (75% and 100% of recommended dose), on crops yields and soil properties under a wheat–fodder maize cropping sequence. Individual addition of organics at a higher level increased yields of wheat and subsequent maize. Soil microbial biomass carbon was enhanced as both a direct and residual effect with the addition of farmyard manure followed by vermicompost and fertilizer treatments, and also by combined addition of manure with either vermicompost or mineral fertilizer. Farmyard manure increased the availability of soil macro- and micronutrients, whereas vermicompost influenced only the availability of micronutrients at wheat harvest. A residual effect of farmyard manure and mineral fertilizers was found for available N. Meanwhile, the residual status of micronutrients in the soil was either maintained or significantly improved due to organic amendments (Mn and Zn with farmyard manure; Fe and Zn with vermicompost). Interaction of farmyard manure and vermicompost at a higher level benefited the next crop by increasing the yield of fodder maize and improving the availability of P and metals in soil.