Sugarcane, a highly productive crop, is frequently challenged by different biotic agents, such as the pokkah boeng disease that can cause drastic yield losses of up to 40%. This airborne fungal disease is caused by various Fusarium species integrated into a complex. Integrating novel compounds and biological control agents is of paramount importance to cope with these fungi in sustainable systems. In this study, we aimed to evaluate the effect and compatibility of phosphite (Phi) and Trichoderma sp. in the control of Fusarium sp., in vitro and in planta. Using in vitro tests, we evaluated the effects of Phi (0, 500, 1000, 2000, 4000, and 8000 µg mL−1) and the compatibility of Phi + Trichoderma (isolates Taz 001, 013, and 016) on the pathogen complex. Using in planta tests, we evaluated the compatibility of Phi + Trichoderma (Taz-016) in the control of Fusarium in sugarcane plants under greenhouse conditions. A synergistic effect of Phi + Trichoderma was observed in vitro on the control of the pathogen, especially when combining 1000 µg mL−1 + Trichoderma Taz-016. In the in planta trial, combining 4000 µg mL−1 Phi + Trichoderma Taz-016 showed the best control of Fusarium infection, improving plant height, culm length and leaf dry weight.