Cold atmospheric pressure plasma (CAP) has been investigated with promising results for peri-implant diseases treatment. However, prior to in-vivo applications of CAP sources in humans, short-term harmful mucosal damage or other unwanted side effects have to be reviewed. 180 male mice (B6C3F1) were divided into twelve treatment groups (n = 15). The right buccal cheek mucosa was treated with CAP. The first and second group each received continuous 10 sec irradiation with 2 different plasma sources (kINPen09, PS-MWM). The third group was treated with the kINPen09 for one minute. Control groups were treated with a corresponding dose of ultraviolet light for 8 seconds or 48 seconds and the other one was left untreated. The animals were weighed before and after treatment. The animals were sacrificed one day or one week after exposure. Stained tissue samples were histologically examined for tissue damage independently by two experienced pathologists. One day after CAP treatment histological analysis showed focal mucosal erosion with superficial ulceration and necrosis accompanied by a mild inflammatory reaction. One week after CAP treatment, the mucosal defects were completely re-epithelialized, associated with remnants of granulation tissue in the stroma irrespective of treatment duration. Furthermore, no cytological atypia was found and no severe weight loss occurred. The control groups did not show any alterations at all. CAP treatment led to a superficial mucosal damage that healed within few days. Nonetheless, further long-term experiments are necessary to exclude undesirable side effects after longer observation time. Particularly, potential carcinogenic effects must be ruled out prior to the application of CAP treatment in daily dental practice.