To mass-produce nutritional kombucha with quality consistency, it is necessary to design synthetic microbial community (SMC) starters with clear bacterial compositions. In this study, a three-species SMC, including Acetobacter pasteurianus, Gluconacetobacter xylinus and Zygosaccharomyces bailii, was designed. Acetic acid bacteria (AAB) in SMC produced a higher concentration of organic acids synergistically compared to each strain inoculated alone. Gluconic acid was the most abundant organic acid in kombucha fermented by SMC, which contributed to the pleasant sour taste of the beverage. AAB could also oxidise the alcohol produced by Z. bailii, making kombucha a soft beverage. Total phenol and flavonoid concentrations increased during fermentation, which enhanced the health benefits of kombucha. The sensory evaluation demonstrated tsshat sensory attributes of SMC fermented kombucha were quite similar to those fermented by the symbiotic culture of bacteria and yeast (SCOBY). Therefore, SMC could be utilised in the industrial mass production of kombucha for better quality control and product consistency.