Preheat the oven to 400°F. Lightly grease a large baking dish or sheet pan and set aside.
In a large bowl, combine the ground beef, eggs, diced onion, ketchup, cheddar cheese, parmesan cheese, almond flour, minced garlic, olive oil, oregano, chili powder, salt, and pepper. Mix just until combined.
Fold in most of the cooked, diced bacon, reserving a small amount for topping.
Wash the bell peppers and slice the tops off. Remove the seeds and ribs from the inside and arrange the peppers upright in the prepared baking dish.
Divide the beef mixture evenly among the peppers, pressing it gently into each one. Top with the reserved bacon and additional cheese if desired.
Bake uncovered for 40–45 minutes, or until the peppers are tender and the filling reaches an internal temperature of 160°F.
Remove from the oven and let rest for 5 minutes before serving.