The control of mixing conditions is one of the prerequisites for the successful fermentation performance of shear sensitive fungal cultures. The Fusicoccin (a biosynthetic plant growth regulator) producing fungus Fusicoccum amygdali Del. grows in the form of large mycelial agglomerates with long peripheral hyphae and partially as filamentous mycelia. The broth is characterized by high viscosity and the non-Newtonian, pseudoplastic flow behaviour, which causes the problems of mixing and mass transfer during fermentation. In this work, an attempt has been made to improve the fusicoccin (FC) production in FU-8 bioreactors using different mixing systems: TMS (The turbine mixing system), CMS1 (The counterflow mixing system with one drive), and CMS2 (The counterflow mixing system with two drives—the upper and lower ones). Higher agitator speed rates were possible in both CMS, since they caused less damage to the hyphae in comparison with TMS. Hydrodynamic conditions in fermenters were controlled using a Stirring Intensity Measuring Device, SIMD-F1. The distribution of the local flow kinetic energy e was analysed in the planes of the maximum mixing intensity. The energy e values in the local intensive planes were higher for TMS in comparison with those for CMS even at lower agitator speed rates of TMS, which could be indicative of an increased shear stress in TMS and obviously caused undesirable morphological changes of F. amygdali and a lowered FC yield. Principal fermentation parameters were analysed. The use of counterflow impellers improved the oxygen transfer efficiency, provided the formation of a more productive morphology, lowered the viscosity of the broth, increased the concentration of the biomass and FC. The improvement of FC production using the optimum mixing system was characterized by higher values of the oxygen uptake rate and lower values of the respiratory quotient during the fermentation. The control of the local mixing intensity using SIMD-F1 gives the possibility to understand the mixing behaviour in bioreactors and, for example, predict the influence of mixing on the mycelial fermentation performance.