I keep things pretty clean when making koji, but I don’t sterilize like one would do in laboratory conditions. The mold grows strong and keeps competitors from establishing. I figure that the occassional bacteria or mold getting in will only enhance the final product. While I keep everything clean, I don’t wash the growing trays between batches. The mold and spores there will help inoculate the next batch which I have inoculated with the lab produced starter (I can use less). After 5 batches, however, the residues start caking up with signs of bacteria infection, so I clean them. 

If it is bad, I could then boil or bake them in the oven at a low temperature to ‘sterilize’ them, but I almost never have to do that. 

The trays are easy to take apart for precise cleaning if neccessary. I have never had to do that.