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Step 1
Preheat the oven to 375 degrees F (190 degrees C). Line a baking sheet with parchment paper.
Step 2
Mix yeast into warm water in a small cup, stirring to dissolve. Set aside.
Step 3
Place 1 1/2 cups mozzarella cheese into a medium microwave-safe bowl. Microwave for 90 seconds, stirring every 30 seconds until completely melted. Stir in the yeast mixture and egg; stir to combine. The mixture will not incorporate well at this point.
Step 4
Stir in almond flour, xanthan gum, and salt. If difficult to mix, reheat in the microwave for 20-30 seconds to soften the cheese. Stir again until well incorporated. Knead dough by hand for 2 minutes.
Step 5
Place dough on the prepared baking sheet and press with your fingers into a thin crust 11 to 12 inches in diameter.
Step 6
Bake in the preheated oven until lightly browned, about 10 minutes. Spread pizza sauce over pizza. Top with remaining 1 1/2 cups mozzarella cheese, then scatter pepperoni on top.
Step 7
Return to the oven and bake until cheese is melted, about 5 minutes more. Sprinkle with red pepper flakes. Cut into 6 slices.