The agro-environmental impact of supplemented biochar manure pellet fertilizer (SBMPF) application was evaluated by exploring changes of the chemical properties of paddy water and soil, carbon sequestration, and grain yield during rice cultivation. The treatments consisted of (1) the control (no biochar), (2) pig manure compost pellet (PMCP), (3) biochar manure pellets (BMP) with urea solution heated at 60 °C (BMP-U60), (4) BMP with N, P, and K solutions at room temperature (BMP-NPK), and (5) BMP with urea and K solutions at room temperature (BMP-UK). The NO3−–N and PO4−–P concentrations in the control and PMCP in the paddy water were relatively higher compared to SBMPF applied plots. For paddy soil, NH4+–N concentration in the control was lower compared to the other SBMPFs treatments 41 days after rice transplant. Additionally, it is possible that the SBMPFs could decrease the phosphorus levels in agricultural ecosystems. Also, the highest carbon sequestration was 2.67 tonnes C ha−1 in the BMP-UK treatment, while the lowest was 1.14 tonnes C ha−1 in the BMP-U60 treatment. The grain yields from the SBMPFs treatments except for the BMP-UK were significantly higher than the control. Overall, it appeared that the supplemented BMP-NPK application was one of the best SBMPFs considered with respect to agro-environmental impacts during rice cultivation.