Sorry but my first response was bleach. But I see you want to stay away from that, maybe vinegar...baking soda. I use baking soda and vinegar for almost all my cleaning needs around the house, I too want to keep it Green, safe, simple and get back to the basics with chemicals in my home. But for mold, nothing works better than bleach. I have had such great success with bleach on my stubborn tile/grout mold that I don't know if there is anything out there that can do better with out spending a FORTUNE. Shakely is expensive. And for the amount of times you really need bleach, i don't think it is worth it to spend that kind of money on a product you don't know will work on mold. I suggest you consult your manual/customer service for the tub, see what it tells you about mold in the jets. It sounds like it is in the tubes inside, then I don't know how you would tackle that besides replacing the tubing/jet mechanisms or filling the tub with water and adding a gallon of bleach and letting the jets run for an hour, I suppose you could try that with vinegar and some baking soda...? Good luck.