Due to their morphology, structure, small size and rapid growth, microorganisms have exceptional potential for synthesis and degradation. Nowadays, microorganisms are used in many sectors, such as food and biological industries, fine chemistry, health, energy, and environmental protection. A bioreactor is a container with different geometries in which biochemical reactions are catalyzed by biological systems, including microorganisms (bacteria, fungi, algae), animal or plant cells, and enzymes. The bioreactors are designed to meet the requirements of the biological systems by regulating different culture conditions, including nutrient concentration, temperature and pH, agitation, and aeration. They are applied in the production of various metabolites, including primary metabolites (amino acids, enzymes, etc.), secondary metabolites (antibiotics, hormones, etc.), or for the biotreatment of solid or liquid wastes. This chapter will mainly review the various types of bioreactors (cell-free and cell-immobilized bioreactors) applied in both metabolite production and pollutant biodegradation processes.