Biochar is stable in soil and can have long-term effects on its physicochemical properties. Hence, a pot experiment was conducted with medium-fertility (MF) and low-fertility (LF) soils after 1 year of rice husk biochar and organic fertilizer application to determine biochar’s residual effects on soil chemical properties, grain yield, and greenhouse gas emissions. In previous years, biochar alone (at application rates of 5 and 10 t ha−1) and biochar combined with chicken manure (CHM) or cow manure (at application rate of 5 t ha−1) were applied to the soil. In the present year, the soils were fertilized with only chemical fertilizers. Results indicated that application of 10 t ha−1 biochar combined with 5 t ha−1 CHM (B10:CHM) produced the highest grain yield and total global warming potential (GWPtotal) in both soils. Regarding grain yield, non-significant results were detected for B10:CHM, B5:CHM, and B10. This study revealed that biochar retains nutrients without annual reapplication and has long-term effects. Although biochar application can suppress N2O emissions effectively, the combined application of biochar 10 t ha−1 and organic manure significantly increased CH4 emissions. Overall, B5:CHM can be recommended for rice cultivation since it improves grain yield without increasing GWPtotal.