Place a large skillet over medium-low heat and add in the olive oil.
Once the oil heats, add in the garlic. Cook garlic for 1 minute and add in the red pepper flakes. Cook for 30 seconds and then add in the chopped onion. Stir and cook for about 2 minutes or until onions begin to soften.
Add in the crushed tomatoes, season generously with salt and pepper and add in the oregano and basil flakes. Stir to combine.
Let cook, stirring occasionally, for about 15 minutes or until the sauce fully reduces.
Once the sauce reduces, add in the zucchini pasta and pepperoni. Cook for about 2 minutes or until zucchini begins to soften and is heated through.
Add in the mozzarella cheese, cook for another 30 seconds, and then pour into a bowl and enjoy!