An attempt was taken for the management of charcoal rot disease of soybean caused by Macrophomina phaseolina using the integration of bio-agent with fungicide and organic amendment. Before going to the field experiments, different in-vitro trials were conducted to select a virulent isolate of M. phaseolina, an effective antagonistic isolate of Trichoderma harzianum, suitable fungicide and organic amendment. Among the seven isolates of M. phaseolina, MSP-4 isolate was selected as the test pathogen by the pathogenicity test. On the contrary, among the eighty-seven isolates of T. harzianum, ISR-26 isolate showed the highest (81.85%) inhibition of radial growth of test pathogen. In the case of fungicidal evaluation trial, Provax 200WP was found the most effective fungicide at the moderate concentration (150 ppm) but the highest conc. of Conza 5%EC and Bavistin 50WP for inhibiting the radial growth of M. phaseolina isolate MSP-4. Additionally, in vitro trial of different organic amendments, mustard oil cake was found the most active organic amendment for reducing the growth (50.92%) and development of test pathogen at 3% concentration level. In the field trial, integrated use of T. harzianum with Provax 200WP and mustard oil cake under the treatment T9 was appeared the best treatment in reducing seedling mortality (80.47%), disease incidence (80.14%) as well as disease severity (88.55%) caused by the test pathogen. Moreover, treatment T9 was the best treatment not only for management of the soybean disease but also increased the significant quantity of yield (104.42%).