I don't know what The Eat Clean diet advocates, can you give some details?
Basically, whole foods is eating foods closest to the natural state as possible, minimally processed foods. Fruits, veggies, legumes, whole grains, etc. And of course there are some trade offs like bread is processed but there is definitely a difference between wonder bread and whole grain bread with a few ingredients in it.
You can't out-exercise poor eating habits.