Baking soda is often effective at reducing or eliminating shoe odor. While sprinkling baking soda in the shoes at night and tapping the shoe to discard it in the morning works, creating a sachet by tying a small amount of powder in the toe of a sock is less messy.
Bacteria, which grows in the moist shoe environment, is the major cause of shoe odor. Eliminate the bacteria by washing and drying shoes if possible. Microwaving wet shoes or wiping their insides with a cotton ball dipped in alcohol sometimes works for shoes that are not washable, and alternating pairs of shoes for daily wear gives them some time to dry between wears.