A method is provided for making a coated article including an anti-bacterial and/or anti-fungal coating. In certain example embodiments, the method includes providing a first sputtering target including Zr providing a second sputtering target including Zn and co-sputtering from at least the first and second sputtering targets to form a layer comprising ZnxZryOz on a glass substrate. A coated article having an anti-bacterial and/or anti-fungal coating made using this method may also be provided.