By absorbing bad smells, baking soda can act as a good deodorizer for shoes and even for feet. You can sprinkle it directly in your shoes and tap it out later, but it may leave traces of white powder. The coffee filters will bypass that issue. Baby powder can be used in place of baking soda.
Another option is to freeze your shoes. Put them in resealable bags to protect them from the extreme temperature inside the freezer. Leave them in the freezer overnight to help kill the bacteria. Take out from the freezer and thaw.