Rehabilitation of open-cast coal mines is a critical intervention for bringing back productive surface soil and sustaining ecosystem functioning. Mining activities not only disturb the key soil properties, but also cause heavy metal contamination. Significantly, 32,000 acres of land in Odisha have been affected by coal mine. In this study, two representative mine areas, Talcher and Jharsuguda in Odisha were selected for our study. The soil physiochemical, available soil nutrient, microbial biomass carbon, soil enzymatic activities and heavy metal contents were estimated in the three sites (rehabilitated, non-rehabilitated and paddy fields) and two soil depth (0–15 and 15–30 cm) of both Talcher and Jharsuguda. The soil pH was higher in rehabilitated sites (5.55 to 8.42) as compared to the paddy fields (5.38 to 5.85) and non-rehabilitated sites (4.16 to 4.57). The average available nitrogen and phosphorus contents were lower in non-rehabilitated sites than the rehabilitated sites and paddy fields. Labile carbon pools (readily mineralizable carbon and microbial biomass carbon), soil enzymatic activities (dehydrogenase and fluorescein di-acetate) were negatively affected by mining activities and it was higher in paddy soil than the rehabilitated and non-rehabilitated sites. Further, the heavy metals (cobalt, copper, iron, and lead) were relatively higher at non-rehabilitated and rehabilitated sites. Heavy metal-based geo-accumulation, integrated pollution and pollution load indices were indicated the possible pollution risk in the rehabilitated study site also. Therefore, we recommend a better technical effort should be made in the top-soil management of coal mine spoil areas during rehabilitation to sustain the productive ecosystem functioning.