Biomicrorobots, inherently motile and self-powered, are promising candidates for biomedical applications, such as targeted drug delivery, since they can actively deliver the therapeutic agent to the tissue or organ of interest, decreasing potential adverse side effects from the systemic distribution of the drug. Magnetotactic bacteria (MTB) have great potential as biomicrorobots since their swimming trajectories can be directed using an applied magnetic field, a phenomenon known as magnetotaxis. The efficacy and limitations of directed navigation via magnetotaxis in conditions which could be experienced within the body must be thoroughly understood to efficiently deliver the drug-loaded cargo to the target location. The motility and directed navigation of these bacteria through intricate microenvironments mimicking the natural microvasculature has not been investigated, nor has magnetotaxis in non-Newtonian fluids, such as those that could be encountered in the body like blood plasma or mucus. Furthermore, applying and accurately controlling a magnetic field within a microscopic region during bacterial magnetotaxis studies at the single-cell level is challenging due to bulky microscope components and the inherent curvilinear field lines produced by commonly used bar magnets. In this dissertation, the development of a custom microfluidic- electromagnetic coils platform is presented for use with an optical microscope to produce controlled, linear magnetic field lines to visualize and acquire images at the single-cell level for magnetotaxis studies in microfluidic devices. In addition, directed navigation of MTB through a vasculature-on-a-chip device and external factors adverse to effective magnetotaxis are demonstrated. Finally, magnetotaxis in mucus-mimicking non-Newtonian solutions is evaluated within microfluidic channels. Overall, the outcomes of this work advance the techniques for MTB magnetotaxis studies and contribute to the growing knowledge of the capabilities of directed navigation by magnetotaxis for potential in vivo applications.