Use a sponge and antibacterial soap to clean ballistic nylon duffle bags. These types of bags will repel dirt and odors relatively easily on their own, so a simple wipe-down is all that is needed. Avoid using chemical based cleansers, as this can damage the bag.
Clean canvas duffle bags with soap and water first, washing the entire bag. Then use laundry detergent to spot-clean any remaining stains.
Blow dry any wet hardware immediately to prevent rusting or discoloration. USA Flight Insurance cautions against oiling hinges or zippers to avoid leaks and damage to clothing.
Spray the inside of the duffle bag with Oust, Febreze, or a preferred air freshener. This will help mask and eliminate odors. Make sure you do not use a harsh, highly chemical fragrance---these may damage the duffle bag.
Use solutions designed to strengthen the resistance properties of nylon and polyester bags. Over time and during cleaning, such resistance can wear off. Additionally, for canvas bags, consider spraying the bag with Scotch Guard to protect from future stains and odors.