The Key to Preventing Smelly Shoes is Eliminating Moisture:

MD Podiatrist
 
According to podiatrist Daniel Michaels, DPM, the leading cause of odor in any type of shoe is moisture, “which leads to a multitude of problems, from odor-causing bacteria to fungal infections of the skin,” he says. Limiting the amount of moisture in the shoe bed and lining of your shoes is critical, he adds, something that you can achieve by wearing the right type of socks or stockings. Oftentimes, lighter-weight and moisture wicking materials, like cotton, can keep your feet from overheating in the first place.
 
 
Dr. Michaels says that work boots and athletic shoes are the most impacted by excess moisture, and are, therefore, often the smelliest pairs in our closets. “After use, these shoes should be placed in a well-ventilated area in an upright position,” he says. “Then, use a disinfectant and deodorizer spray on the insole and liner.” If your shoes or boots are particularly wet, he suggests removing the liners entirely; leave them out to dry over night. They should be complete moisture-free before you slip them back into your shoes.