Prep a baking sheet: Line a rimmed sheet with parchment and lightly oil it.
Preheat the oven to 400°F (200°C). If pan-searing, heat a large skillet over medium with olive oil instead.
Mix the base: In a large bowl, combine ground chicken, Parmesan, almond flour, egg, onion, garlic, parsley, Italian seasoning, red pepper flakes, salt, black pepper, and tomato paste. Stir gently with a fork or your hands until just combined.
Form the meatballs: Scoop about 2 tablespoons of mixture per meatball.
If stuffing, flatten slightly, tuck a mozzarella cube inside, and seal well. Roll into smooth balls.
Choose your cook method: Oven: Arrange on the prepared sheet and bake 12–15 minutes, until lightly golden and almost cooked through.
Skillet: Sear in batches for 2–3 minutes per side until browned. They don’t need to be fully cooked yet.
Simmer in sauce: Warm marinara in a large oven-safe skillet or pot.
Nestle the meatballs into the sauce and simmer 5–8 minutes, until they reach 165°F (74°C) internally.
Finish with cheese: Sprinkle extra Parmesan and a little shredded mozzarella over the top. Cover for 2 minutes to melt, or broil briefly until bubbly.
Garnish and serve: Top with fresh basil or parsley. Serve over zucchini noodles, spaghetti squash, roasted broccoli, or a crisp green salad.