I have that problem. I tried baking soda. It works for me. Before I go to bed, I cover the sole of the shoes with baking soda. Next morning, I get rid of the baking soda in the toilet. I hold the shoes close to the toilet as it gets dusty with baking soda.
Also, you could put your shoes in a zipper lock bag and put it in the freezer overnight. The cold temperature kills the smelling bacteria. I never tried this one.