The influence of oxygen (and argon) plasma cleaning and a base-acid cleaning procedure on stainless steel surfaces was studied. The main aim was to clean stainless steel samples from Paracoccus seriniphilus biofilms without changing the surface properties which are relevant for bacterial attachment to allow reuse in a biofilm reactor. It is shown that oxygen plasma cleaning, which very successfully removes the same kind of biofilm from titanium surfaces, is not suitable for stainless steel. It largely influences the surface chemistry by producing thick metal oxide layers of varying compositions and changing phenomenological surface properties such as wettability. A promising method without changing surface properties while cleaning satisfactorily is a combination of base and acid reagents at elevated temperature.