Preheat and prep: Heat your oven to 400°F (200°C). Lightly oil a large baking dish or sheet pan.
If using add-ins like peppers or mushrooms, sauté them in a little olive oil until softened and set aside to cool.
Mix the base: In a large bowl, whisk the eggs, heavy cream, Italian seasoning, garlic, salt, pepper, and red pepper flakes. Stir in almond flour and Parmesan until you have a thick, seasoned slurry.
Add the meat and mix gently: Add ground beef and pork to the bowl. Sprinkle in the onion (or onion powder), chopped pepperoni, and 1 cup of the mozzarella.
Use your hands to mix with a light touch until just combined. Don’t overmix or the meatballs can get dense.
Form meatballs: Scoop into 18–20 golf ball–sized meatballs (about 2 tablespoons each). Roll lightly and place them on the prepared pan with space between.
Bake the first round: Bake for 15 minutes until the outsides are just starting to brown and the meatballs hold their shape.
Add sauce and cheese: Remove the pan. Pour marinara around the meatballs, spooning a little over the tops.
Sprinkle the remaining 1/2 cup mozzarella over everything. If using olives or peppers on top, add them now.
Finish baking: Return to the oven for 10–12 minutes, until the cheese melts and the sauce bubbles. Internal temp should reach 160°F (71°C).
Rest and garnish: Let the meatballs rest 5 minutes.
Sprinkle with chopped basil or parsley. Serve hot with extra Parmesan if you like.