Preheat your oven to 375°F (190°C). Generously spray a 12-cup muffin tin with non-stick cooking spray or line with parchment paper liners for easier cleanup.
Prepare the mix-ins. In a large skillet over medium heat, sauté the onion and bell pepper until softened, about 5 minutes. Add the garlic and cook for an additional 30 seconds until fragrant. Set aside to cool slightly.
Combine all ingredients. In a large mixing bowl, gently combine the ground beef, ground turkey, breadcrumbs, Parmesan cheese, cooled vegetables, eggs, tomato paste, basil, oregano, Italian seasoning, salt, pepper, and red pepper flakes (if using). Mix with your hands just until combined—don't overmix or your meatloaves will be tough.
Form the mini loaves. Divide the mixture evenly among the 12 muffin cups. The cups should be filled to the top but not mounded above the rim.
Create a sauce indent. Use your thumb or the back of a spoon to make a small indentation in the top of each meatloaf bite. This will hold the sauce later.
Bake the first round. Place the muffin tin in the preheated oven and bake for 15 minutes.
Add the toppings. Remove the meatloaf bites from the oven. Spoon about 2 teaspoons of marinara sauce into the indentation on each meatloaf, then sprinkle with mozzarella cheese.
Finish baking. Return to the oven and bake for an additional 5-10 minutes, until the cheese is melted and bubbly and the internal temperature of the meatloaves reaches 165°F (74°C).
Rest briefly. Allow the meatloaf bites to rest in the pan for 5 minutes. This helps them set up and makes them easier to remove.
Garnish and serve. Carefully remove the mini meatloaves from the tin using a spoon or knife to loosen the edges if needed. Sprinkle with fresh basil and serve warm.