You need to use an enzymatic cleaner like Nature’s Miracle (definitely found at pet stores, but places like Walmart or even a supermarket might carry it as well). It will work, but the smell will get worse for a bit before it gets better.
For what it’s worth, we’ve raised 5 puppies so far and never used training pads - we kept them in crates and if they needed out in the middle of the night we woke up and took them out (most didn’t after the first week or so). I think using training pads turns housebreaking into a 2 step process ... first they need to learn to use the pads then they need to learn not to use pads and to go outside. Makes more sense to me to just teach them to go out in the first place.