Preheat oven to 400 degrees.
Wash the beets, and cut off any roots and stems. Then, wrap the beets in aluminum foil and bake them for 45 minutes, or until tender.
When beets are baked through, remove them from the oven and let them cool until they are okay to handle by hand.
Then, unwrap the foil off the beets. Peel off any beet skin with a peeler. Then, place the beets in a high-powered blender. Blend on high until beets are puréed. This should result in about 1 and 1/4 cups of puréed beets.
Add the puréed beets to a bowl along with the salt, egg, gluten-free flour, almond meal, baking powder, and egg and mix well, using a spatula. The dough will be wet.
Using the spatula, smooth out beet crust to about 1/3 inch thick onto a parchment-lined baking tray.
Bake the beet crust for 25 minutes.
Take out and top with cheese, veggies, and more cheese.
Bake for another 10–15 minutes, until the cheese is melted.
Slice the beet pizza, sprinkle it with some dried oregano and red chili flakes, and enjoy!