The increase in soil carbon sequestration under long-term no-till (NT) and cover crop management has been shown to form part of a sustainable agricultural management practice system. Along with the increase in soil organic carbon (SOC), soil respiration in this system was also enhanced by the increased soil temperature through the decomposition that causes carbon loss from the soil. To overcome this issue, biochar can be applied. However, the addition of biochar into this system is not well studied. Therefore, the aim of this study was to investigate the effect of this system on soil respiration. The experiment was conducted at the Center for International Field Agriculture Research & Education, Ibaraki University. Long-term tillage practices, such as NT and moldboard plowing (MP), cover crops such as rye (RY) and fallow (FA), and biochar application such as with biochar (WB) and no biochar (NB) were applied to a split-split plot in a randomized complete block design with four replications. The daily CO2 flux was measured every week at 9:00-11:00 a.m. The daily soil respiration was affected by tillage and cover crop with NT practice had significantly higher daily CO2 flux than that of MP (23.8%-107.4% and 38.0%-107.8%), while RY had higher flux than that of FA (11.9%-81.2% and 34.9%- 65.4%) in 2020 and 2021 soybean growing season, respectively. Additionally, in the 2020 cover crop growing season RY also increased daily CO2 flux approximately 41.8%-88.2% compared to FA. Biochar addition significantly reduced soil respiration in soybean and cover crop seasons compared to NB by 24.0%-50.7% and by 25.9%-48.3%, respectively. This reduction in soil respiration by the biochar decreased annual CO2 emissions by 17.6% and 13.0% in 2020 and 2021. The values of these emissions ranged from 9.6 Mg ha-1 for MP FA WB to 18.9 Mg ha-1 for MP RY NB in 2020 and from 7.5 Mg ha-1 for MP FA WB to 13.7 Mg ha-1 for NT FA NB in 2021. This study highlights the crucial role of biochar in reducing soil respiration and enhancing SOC sequestration. The addition of biochar into this system was able to reduce soil respiration by regulating the soil temperature, soil moisture, and protect the SOC from decomposition. Biochar addition also increased the SOC and decreased the soil bulk density, which improves soil porosity. Therefore, these findings would be very useful to be included within the global scenario of soil organic matter management.