Wear socks. The Centers for Disease Control recommends that you always wear socks with your shoes. Cotton and wool socks are the best for keeping your feet and insides of your shoes dry. Wearing socks may help reduce the odor coming from your shoes, however, as the socks get damp you will want to change them throughout the day.
Apply powder inside the shoes. Use an anti-fungal or drying powder inside the shoes after each time you wear them to absorb any moisture left behind. This will also help you from getting athlete's foot from wearing your sneakers without socks. Baking soda can also be used, and it provides a cheaper method for absorbing moisture from your sneakers.
Wash sneakers regularly. Place sneakers in the washer every one to two weeks to clean out and disinfect the inside. An alternative to regularly washing your sneakers is to place a cotton ball soaked in clove oil, or other essential oil, inside the sneakers. A fresh dryer sheet placed in your sneakers every night will give them the scent of being just washed.
Purchase removable insoles. Removable soles can be used for more than just offering your foot extra arch support. Take out the removable soles on a nightly basis, and let them completely air dry before reinserting them into your sneakers. When airing the soles out, you can also air out the sneaker by loosening up the laces and puling out the tongue. Replace the soles with new ones as the odor gets stronger.