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Biochar is a carbon-rich material prepared from the pyrolysis of biomass under various conditions. Recently, biochar drew great attention due to its promising potential in climate change mitigation, soil amendment, and environmental control. Obviously, biochar can be a beneficial soil amendment in several ways including preventing nutrients loss due to leaching, increasing N and P mineralization, and enabling the microbial mediation of N2O and CO2 emissions. However, there are also conflicting reports on biochar effects, such as water logging and weathering induced change of surface properties that ultimately affects microbial growth and soil fertility. Despite the voluminous reports on soil and biochar properties, few studies have systematically addressed the effects of biochar on the sequestration of carbon, nitrogen, and phosphorus in soils. Information on microbially-mediated transformation of carbon (C), nitrogen (N), and phosphorus (P) species in the soil environment remains relatively uncertain. A systematic documentation of how biochar influences the fate and transport of carbon, phosphorus, and nitrogen in soil is crucial to promoting biochar applications toward environmental sustainability. This report first provides an overview on the adsorption of carbon, phosphorus, and nitrogen species on biochar, particularly in soil systems. Then, the biochar-mediated transformation of organic species, and the transport of carbon, nitrogen, and phosphorus in soil systems are discussed. This review also reports on the weathering process of biochar and implications in the soil environment. Lastly, the current knowledge gaps and priority research directions for the biochar-amended systems in the future are assessed. This review focuses on literatures published in the past decade (2009–2021) on the adsorption, degradation, transport, weathering, and transformation of C, N, and P species in soil systems with respect to biochar applications.