Preheat the oven: Set to 400°F (200°C). Line a sheet pan with parchment or lightly grease a baking dish.
Make the meat mixture: In a large bowl, mix ground meat, egg, Parmesan, almond flour, onion powder, garlic powder, oregano, basil, red pepper flakes, salt, and pepper. Use your hands to combine gently.
Don’t overmix.
Prep the fillings: Cut mozzarella into small cubes. If using pepperoni, chop into small bits.
Form the meatballs: Scoop about 2 tablespoons of the meat mixture into your hand. Flatten slightly, place a mozzarella cube (and a little pepperoni) in the center, then wrap the meat around it to seal completely.
Roll to smooth. Repeat with the rest.
Arrange and bake: Place meatballs on the prepared pan with a bit of space between them. Bake for 15 minutes.
Add sauce: Remove from the oven, spoon marinara around and lightly over the meatballs.
Return to the oven for 8–10 more minutes, until the centers reach 160°F and the cheese is melty.
Finish and serve: Rest 5 minutes. Garnish with chopped parsley or basil. Serve with extra sauce and a sprinkle of Parmesan.