Prep the peppers: Preheat the oven to 375°F (190°C). Slice the tops off the peppers, remove seeds and membranes, and trim the base if needed so they stand upright.
Place them in a baking dish, snug but not crammed.
Par-bake for tenderness: Add 1/4 cup water or broth to the baking dish. Cover tightly with foil and bake for 10 minutes. This softens the peppers so they don’t stay crunchy later.
Remove and set aside.
Sauté the aromatics: Heat olive oil in a large skillet over medium heat. Add onion with a pinch of salt and cook 3–4 minutes until translucent. Stir in garlic and cook 30 seconds until fragrant.
Brown the beef: Add ground beef, breaking it up with a spatula.
Season with salt and pepper. Cook until no longer pink and most moisture has evaporated, about 5–7 minutes.
Add seasonings and sauce: Stir in oregano, basil, smoked paprika, and red pepper flakes. Mix in tomato paste and cook 1 minute to caramelize slightly.
Add tomato sauce and simmer 2–3 minutes to thicken.
Fold in cauliflower rice: Add riced cauliflower to the skillet. Cook 2–3 minutes, stirring, until it absorbs flavor and softens. Taste and adjust salt and pepper.
The mixture should be savory and not watery.
Cheese it up: Off the heat, stir in half the mozzarella and all the Parmesan. This helps the filling hold together and stay moist.
Fill the peppers: Spoon the beef mixture into each pepper, packing it gently and mounding slightly. Top with the remaining mozzarella.
Bake: Return the dish to the oven, uncovered, for 18–22 minutes, until the peppers are tender and the cheese is melted and lightly golden.
Finish and serve: Let rest 5 minutes so the filling sets.
Garnish with chopped parsley or basil. Serve warm.