Preheat oven to 375°F (190°C). Lightly grease a 9x13-inch baking dish.

In a large skillet over medium-high heat, cook the ground beef with diced onion until no pink remains and the onion is soft.

Drain excess fat, then add garlic and bell pepper; cook 2 minutes more.

Stir in crushed tomatoes, Italian seasoning, and red pepper flakes. Simmer 5 minutes so flavors meld. Season with salt and pepper.

In a large bowl, combine cauliflower rice, almond flour, beaten eggs, half the mozzarella, and half the Parmesan. Mix until well combined.

Spread half the cauliflower mixture into the bottom of the prepared dish, pressing lightly.

Spoon the meat sauce over it, then distribute chopped pepperoni across the surface.

Top with the remaining cauliflower mixture, then sprinkle remaining cheeses over the top.

Cover loosely with foil and bake for 20 minutes.

Remove foil and bake another 10–12 minutes, until cheese is golden and edges are bubbly.

Let the casserole sit for 5–10 minutes before slicing. Garnish with fresh basil and serve warm.