Display omitted •Rod-shaped cell harvesting by cross-flow microfiltration with static mixer is investigated.•Radial mixing hindered the shear-induced arrangement of Bacillus velezensis cells.•Flux improvement up to 300% was achieved and it coincides with reduction in specific energy consumption.•Bacillus velezensis cells retained viability.•Microfiltration parameters were optimized using RSM and GA. Substitution of synthetic agrochemicals with bio pesticides, due to the hazards of pollution, has put attention on the development of cost-effective solutions for their production. Membrane fouling remains an immense problem for cross-flow microfiltration implementation in bio-control agent production. The shear-induced arrangement of rod-shaped bacterial cells results in the creation of the brick-like wall layer in filtration cake that has denser packing, and a higher tortuosity, which leads to higher cake resistance. From this perspective, applying turbulent flow by increasing cross-flow velocity is a possible method for the reduction of cake resistance, controlling the filtration performance, which in turn results in higher energy consumption. Turbulence promoters can be positioned into a channel of tubular membranes to reduce cake resistance and consequently increase permeation flux. Radial mixing caused by the turbulence promoter has contributed to disturbance of the shear-induced arrangement of cells and the flux improvement was in the range between 50% to approximately 300%, depending on experimental conditions. Static mixer i.e. turbulence promoter caused higher permeate fluxes at same specific energy consumption, without loss of cell viability due to an increase in shear rate. Microfiltration parameters were optimized using response surface methodology and genetic algorithm.