Biochar application is currently considered to be an effective soil organic carbon (SOC) management to prevent land degradation by enhancing SOC stock. However, quantitative information on the impact of biochar application on carbon dioxide (CO2) flux and associated microbial responses is still scarce, especially in degraded tropical agroecosystems. Here, we evaluated the impact of land management (control (C), biochar (B; 8.2 Mg C ha−1), farmyard manure (FYM) (M; 1.1 Mg C ha−1 yr−1), and a mixture of both (BM; 8.2 Mg biochar-C ha−1 and 1.1 Mg FYM-C ha−1 yr−1)) on CO2 flux, SOC stock, microbial biomass C (MBC), and metabolic quotient (qCO2) in degraded tropical alkaline cropland of southern India, based on a 27-month field experiment. Cumulative CO2 flux over the experiment was 2.4, 2.7, 4.0, and 3.7 Mg C ha−1 in the C, B, M, and BM treatments, respectively. Biochar application increased soil moisture and SOC stock, though did not affect CO2 flux, MBC, and qCO2, indicating the limited response of microbes to increased soil moisture because of small amount of SOC. Combined application of biochar and FYM did not increase CO2 flux compared with FYM alone, due to little difference of microbial responses between the M and BM treatments. Additionally, SOC increment (8.9 Mg C ha−1) and the rate of C-input retention in soil (0.78) was most significant in the BM treatment. Hence, the combined application of biochar and FYM could be sustainable land management by efficient increase of SOC stock in the tropical degraded cropland.