Commercial manufacturing of prebiotics relies on diverse processing steps tailored to the raw material and finished product. Commercial manufacturing operations are distinct from processes suggested in the research literature, accounting for scalability, cost and environmental metrics, and process reproducibility. Common prebiotic production processes involve extraction, hydrolysis using enzymes, acids or hot water, synthesis, condensation polymerization and precision fermentation. Crude extracts are purified using ion exchange, activated carbon, and membrane separation processes to remove impurities and produce prebiotic oligosaccharides with the targeted composition and degree of polymerization. Purified extracts are often concentrated using evaporation systems and may be dried or crystallized to produce a dry finished product. Though not an all encompassing list of prebiotics, detailed descriptions of processes for the production of some of the more common prebiotics, including acacia, fructo-oligosaccharides (FOS), galacto-oligosaccharides (GOS), human milk oligosaccharides (HMOs), inulin, mannan-oligosaccharides (MOS), certain types of resistant starch (RS), xylo-oligosaccharides (XOS), and arabinoxylan oligosaccharides (AXOS) are provided in this manuscript, along with descriptions of commercial scale unit operations that may be applied more generally to newer compounds being investigated for their prebiotic properties. The unique attributes of each type of prebiotic and prebiotic formulation, particularly the degree of polymerization and chemical structure, are strongly controlled by the processes employed in their manufacture. Strategic selection of enzymes (or hydrolysis processes in general), fermentation systems, and extraction systems/solvents will influence the product composition and degree of polymerization, leading to a diverse array of products. Regulatory requirements and quality control systems employed during manufacturing of prebiotics ensure that finished products are safe and effective for consumers, delivering the expected health and physiological benefits.