Kombucha is widely consumed as black tea fermented for 7–14 days. The aim of the present study was to compare the antimicrobial activities of two kombucha beverages originating from green and black teas fermented for 21 days and to characterize the antimicrobial compounds (heat resistance and pH stability). Green and black tea infusions were fermented with a traditional kombucha culture. The resulting kombucha antibacterial/antifungal activities against some pathogenic microorganisms, including human pathogenic bacteria and clinical Candida species, were investigated using the agar diffusion method. The results showed interesting antimicrobial potentials of both experimented kombucha teas against the tested microorganisms, except Candida krusei. The green fermented tea exhibited the highest antimicrobial potential. Indeed, it showed large inhibition zones against Staphylococcus epidermidis (22 mm), Listeria monocytogenes (22 mm) and Micrococcus luteus (21.5 mm). Furthermore, interesting anti-Candida potential was revealed by the reaction of green tea kombucha against Candida parapsilosis.