Shallot productivity in Brebes remains below its potential due to moler disease caused by acid soil. Hence, it’s beneficial to use biological agents to mitigate the risk and to improve shallot growth. This study aimed to examine the growth of shallot and the effect of biological agents on moler pathogens in acid soils. The method used for in vivo experiment was a Randomized Complete Block Design (RCBD) with 3 factors and 4 replications. The first factor was Trichoderma sp., Gliocladium sp., and without biological agent. The second factor was without Fusarium oxysporum f.sp cepae (FOCe) inoculation and with FOCe inoculation. The third factor was soil  pH (2.0-4.5; 5.0-6.5 and 7.0-9.0). The in vitro experiment was conducted to see the antagonism ability towards the pathogen. The data obtained were analyzed by Analysis of Variance and continued with the Duncan’s Multiple Range Test with significance level of 5%. The result showed that the intensity of soil acidity increased the severity of the disease and reduced the growth of shallot plants. Soils with pH (2.0-4.5) or pH (7.0-9.0) accelerated the incubation period and Area Under the Disease Progress Curve (AUDPC). Soils with pH (2.0-4.5) or pH (7.0-9.0) reduced in dry weight, and shallot bulb’s weight. Trichoderma sp. better than Gliocladium sp. in reducing the intensity of the disease and decreasing incubation period. Trichoderma sp. was able to increase the shallot bulb compared to Gliocladium sp. in acid condition.