Prep the noodles If using zucchini noodles, lightly sauté them in a pan with 1 tsp olive oil for 2–3 mins. Drain excess water. If using shirataki or palm pasta, rinse well and dry.
Make the sauce In a large skillet, heat olive oil over medium heat. Add onions (if using) and garlic, and sauté until fragrant.
Add marinara & spices Stir in marinara sauce, Italian seasoning, chili flakes, salt, and pepper. Let it simmer for 3–4 mins.
Add pepperoni Toss in pepperoni slices and let them warm through (they’ll release flavor into the sauce).
Combine everything Add the noodles to the pan, mix well, then sprinkle mozzarella and parmesan cheese on top. Cover and let the cheese melt.