Prep your oven and pan: Preheat the oven to 375°F (190°C). Lightly oil a baking dish large enough to hold the peppers upright.
Prepare the peppers: Slice off the tops and remove seeds and membranes.
If they wobble, shave a thin slice from the bottom so they stand. Place them in the baking dish, cut side up.
Soften the peppers (optional but recommended): Add about 1/4 cup water to the bottom of the dish, cover with foil, and bake for 10–12 minutes. This jump-starts tenderness.
Drain any water left in the dish.
Sauté aromatics: In a large skillet over medium heat, warm the olive oil. Add onion 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 as it cooks.
Season with salt, black pepper, Italian seasoning, paprika, and red pepper flakes if using. Cook until browned with no pink remaining, about 6–8 minutes. Drain excess fat if needed.
Build the filling: Reduce heat to low.
Stir in tomato sauce and simmer 2 minutes. Fold in cooked rice and 1/2 to 1 cup of shredded cheese. Taste and adjust seasoning.
The mixture should be saucy but not soupy.
Stuff the peppers: Spoon the filling into each pepper, packing it gently. Mound slightly above the rim. Top with the remaining cheese.
Bake: Cover loosely with foil and bake for 15 minutes.
Uncover and bake another 10–15 minutes, until the peppers are tender and the cheese is browned and bubbly.
Finish and serve: Let rest 5 minutes. Garnish with chopped parsley or basil. Serve as-is or with a side salad or garlic bread.