Magnetotactic bacteria (MTB) naturally synthesize magnetic nanoparticles that are wrapped in lipid membranes. These membrane-bound particles, which are known as magnetosomes, are characterized by their narrow size distribution, high colloidal stability, and homogenous magnetic properties. These characteristics of magnetosomes confer them with significant value as materials for biomedical and industrial applications. MTB are also a model system to study key biological questions relating to formation of bacterial organelles, metal homeostasis, biomineralization, and magnetoaerotaxis. The similar size scale of nano and microfluidic systems to MTB and ease of coupling to local magnetic fields make them especially useful to study and analyze MTB. In this Review, a summary of nano-and microtechnologies that are developed for purposes such as MTB sorting, genetic engineering, and motility assays is provided. The use of existing platforms that can be adapted for large-scale MTB processing including microfluidic bioreactors is also described. As this is a relatively new field, future synergistic research directions coupling MTB, and nano-and microfluidics are also suggested. It is hoped that this Review could start to bridge scientific communities and jump-start new ideas in MTB research that can be made possible with nano-and microfluidic technologies.