Combine the yeast, honey, and water in a medium bowl and stir. Allow to rest for 10-15 minutes or until the mixture becomes frothy.
In a large bowl fitted to a stand mixer with a hook attachment, combine the almond flour, coconut flour, whey protein isolate, psyllium husk powder, baking powder, and salt.
Next, add the olive oil and yeast mixture to the bowl and mix on medium speed until fully combined.
Using your hands, form the dough into a ball in the bowl and rub olive oil all around the outsides. Cover with plastic wrap and place the bowl in a warm place to rise for 1 hour.
Heat your oven to 400°F. Lightly grease a 10-inch springform cake pan, cast iron skillet, or pie pan.
Rub some olive oil on your hands and spread the dough out into your pan/skillet. Make sure the dough fully covers the bottom and also push it up the sides so that the dough is no more than 1/4-inch thick.
Bake for 5 minutes in the oven then carefully remove and set aside .
Heat a large skillet over medium heat and add in the olive oil, garlic, and onions. Sauté for 3 minutes or until softened, then add in the diced tomatoes, oregano, basil, and red chili flakes. Cook for 10 more minutes until most of the liquid has cooked off and the tomatoes begin to break apart and become jammy.
Assemble your pizza by placing half of the mozzarella cheese in the par-baked crust, followed by half of the cooked meat of your choice, and then half of the tomato sauce mixture. Repeat the process again by layering the remaining meat, followed by the remaining cheese, and the remaining tomato sauce mixture.
Sprinkle with the grated Parmesan over top, then bake again for 10-12 minutes or until the cheese is melted, the inside is hot, and the crust has turned golden brown.
Serve while hot.