Finely dice the onion into 1/4-inch pieces and mince the garlic cloves. Measure out the marinara sauce, grate the parmesan cheese fresh (this helps it melt more evenly into the filling), and preheat your oven to 350°F. Grease a 9x13 inch baking dish with a light coating of oil or cooking spray. Having everything prepped and ready before you start cooking will keep the workflow smooth and prevent the beef from overcooking while you're still dicing vegetables.

Heat a large skillet over medium-high heat and add the ground beef, breaking it apart as it cooks. Once the beef is mostly cooked through (about 5-7 minutes), add the diced onion from Step 1 and continue cooking for another 2-3 minutes until the onion softens slightly. Add the minced garlic, garlic powder, Italian seasoning, and red pepper, stirring constantly for about 1 minute until fragrant. Drain off any excess fat from the pan and season with salt and pepper to taste. The beef should be fully browned with no pink remaining.

Bring a large pot of salted water to a boil and add the manicotti shells. Cook according to package directions until al dente (usually 8-10 minutes)—don't overcook or the shells will become too soft to handle when filling. Drain the pasta gently in a colander and set aside. I always use Barilla shells because they hold their shape better than other brands, especially when they're being filled and baked.

In a large mixing bowl, combine the ricotta, 2.5 cups mozzarella, the freshly grated parmesan from Step 1, and the ground beef mixture from Step 2. Stir until everything is evenly combined, then season with the ground nutmeg, salt, and pepper to taste. The mixture should be creamy but hold together when scooped. This is your filling base that will go into each cooked shell.

Spread 1.5 cups of the marinara sauce evenly across the bottom of your prepared baking dish. Using a spoon or small piping bag, carefully fill each cooked manicotti shell from Step 3 with the ricotta filling mixture from Step 4, then arrange them seam-side up in a single layer in the baking dish. Pour the remaining marinara sauce over the top of the shells, making sure they're well covered. Sprinkle the 1.25 cups mozzarella evenly over the entire top. I prefer to leave a tiny bit of the sauce visible between shells rather than completely burying them—this helps them cook more evenly.

Place the assembled baking dish in the preheated 350°F oven and bake for 25-30 minutes, until the cheese on top is melted and bubbly and the sauce is bubbling around the edges. Let the manicotti rest for 5 minutes out of the oven before serving—this allows the filling to set slightly so it doesn't spill out when plated. Serve with extra marinara sauce on the side if desired.