Preheat oven to 375°F (190°C). Cut each bell pepper in half lengthwise, remove seeds and membranes, and place cut-side up in a 9x13-inch baking dish.
Heat olive oil in a large skillet over medium-high heat. Add onion and garlic; sauté until softened, 2–3 minutes. Add ground beef; cook, breaking it apart, until browned and no longer pink, about 5–6 minutes, ensuring it reaches an internal temperature of 160°F (71°C). Drain any excess fat if needed.
Stir in drained diced tomatoes, oregano, basil, salt, pepper, and red pepper flakes. Cook for 2 minutes. Add chopped spinach and stir until wilted, about 1 minute. Remove skillet from heat.
Fold in the cooked quinoa and 1/2 cup of the crumbled feta until evenly mixed. Taste and adjust seasoning if desired.
Spoon the beef-quinoa mixture generously into each pepper half, mounding slightly. Sprinkle the remaining 1/4 cup feta on top of each stuffed pepper.
Cover the baking dish with foil and bake for 20 minutes. Remove foil and bake an additional 5–10 minutes, until peppers are tender and cheese is lightly golden.
Remove from oven, let rest 2 minutes, then sprinkle with fresh parsley. Serve hot with lemon wedges on the side.