Reinfection in endodontically treated teeth is linked to the complexity of the root canal system, which is problematic to reach with conventional disinfection methods. As plasma is expected to have the ability to sanitize narrow areas, the aim of this study was to analyze the effect of cold atmospheric pressure plasma (CAP) on Candida albicans in root canals of extracted human teeth. CAP was applied as mono treatment and in combination with standard endodontic disinfectants (sodium hypochlorite, chlorhexidine and octenidine). Disinfection efficiency was evaluated as reduction of the logarithm of colony forming units per milliliter (log 10 CFU/mL) supported by scanning electron microscopy as imaging technique. Plasma alone showed the highest reduction of log 10 CFU, suggesting the best disinfection properties of all tested agents.