This article demonstrates a new approach enabling the active control of swimming trajectories of flagellated bacteria in space and time. Bacteria were mixed with water solutions of disodium cromoglycate (DSCG), a lyotropic chromonic liquid crystal (LCLC) that mimics the anisotropic properties of many biological environments. It has been well established that the bacteria then swim in the direction of the self-aligned molecular aggregates of DSCG. It is also known that this host material possesses a diamagnetic anisotropy enabling the control of the local orientation of these aggregates with magnetic fields (MF). This double coupling (bacteria-LCLC & LCLC-MF) allows the efficient real-time control of the orientation of bacterial trajectories. Such control over the motility of microorganisms opens numerous avenues for their manipulation and study, for example, in a lab-on-a-chip device.