If you have a soil substrate, you want micro and macro fauna to eliminate waste products and control mold, fungal, and bacterial growth. Springtails (tropical or temperate) and isopods are frequently used for this purpose, and in addition I personally use red wiggler compost worms to help turn over the soil.
Without some sort of clean up crew, you'll need to do fairly frequent substrate changes in order to maintain a safe environment. Just because it looks and smells okay doesn't mean that it's safe for your chameleon.