Three Cheese Manicotti with Homemade Sauce

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This Three Cheese Manicotti is stuffed with a creamy ricotta filling and baked in homemade tomato sauce. A cozy family dinner ready in just over an hour.

A plated serving of two manicotti rolls covered in red sauce and cheese, cut open with a fork to show the white ricotta filling inside.

Baked Manicotti with Ricotta and Mozzarella
Ingredients
How To Make Baked Three Cheese Manicotti
Top Recipe Tips
High Altitude Adjustments
Baked Three Cheese Manicotti Recipe
Recipe FAQs

Baked Manicotti with Ricotta and Mozzarella

There is something special about a baking dish full of pasta bubbling in the oven. This Three Cheese Manicotti is a comforting dinner that feels like a hug on a plate. It features large pasta tubes stuffed with a rich blend of ricotta, mozzarella, and Parmesan.

While you can use jarred sauce in a pinch, this recipe includes a quick homemade tomato sauce using San Marzano tomatoes. The sauce is bright and garlicky, which cuts through the richness of the cheese filling perfectly. It is a meal that works just as well for a casual family dinner as it does for feeding a crowd at a gathering.

An overhead view of the full baked casserole dish, featuring golden melted cheese, rich tomato sauce, and a garnish of fresh chopped basil.

Ingredients

Manicotti Shells: You need an 8-oz package. Cook them according to the package directions, but be careful not to overcook them, as they need to hold their shape during filling.
San Marzano Tomatoes: The sauce starts with 2 cans (28 oz each) of whole peeled tomatoes. San Marzano-style tomatoes are sweeter and less acidic than standard canned tomatoes.
Ricotta Cheese: Use 3 cups of part-skim ricotta.
Mozzarella & Parmesan: You will need shredded mozzarella and grated Parmesan for both the filling and the topping.
Eggs: Two beaten eggs act as a binder, keeping the cheese filling from running out of the pasta shells.
Fresh Herbs: Fresh basil and parsley add a pop of color and freshness that dried herbs cannot match.

How To Make Baked Three Cheese Manicotti

Cook the manicotti, prepare a simple tomato and basil sauce, mix the three-cheese filling, assemble everything in a baking dish, then bake until bubbling, then finish under the broiler for a lightly browned top.

Prep the Pasta and Oven

Boil: Cook the manicotti shells according to the package instructions. Drain them carefully. Transfer the cooked pasta to wax paper or foil sprayed with nonstick spray and let them cool.
Preheat: Move your oven rack to the middle position. Preheat the oven to 375°F.

Cooked and drained manicotti pasta shells arranged on a baking sheet to cool slightly before filling.

Make the Tomato Sauce

Pulse Tomatoes: Add one can of tomatoes (with their juice) to a food processor. Pulse 3 to 4 times. You want them coarsely chopped, not pureed. Transfer to a bowl and repeat with the second can.
Sauté: Heat 2 tablespoons of olive oil in a large saucepan over medium heat. Add the 3 minced garlic cloves and ½ teaspoon red pepper flakes. Cook for about 1 minute until fragrant.
Simmer: Stir in the chopped tomatoes and ½ teaspoon salt. Bring the mixture to a simmer and cook for about 15 minutes. The sauce should thicken slightly. Stir in 2 tablespoons of chopped fresh basil. Taste and add more salt if needed.

A three-step process shot showing the sauce preparation: blending the tomatoes, sautéing garlic and red pepper flakes in a pan, and simmering the finished tomato sauce.

Make the Filling

Mix: In a medium bowl, combine 3 cups ricotta, 2 cups shredded mozzarella, 1 cup grated Parmesan, 2 beaten eggs, 2 tablespoons chopped basil, 2 tablespoons chopped parsley, ¾ teaspoon salt, and ½ teaspoon black pepper. Stir until the mixture is completely combined.

Two images showing the filling instructions: a glass bowl containing unmixed ricotta, eggs, and herbs, next to the bowl with the ingredients fully combined into a creamy filling.

Assemble and Bake

Base Layer: Spread about 1½ cups of the tomato sauce evenly over the bottom of a 9×13-inch baking dish.
Fill: Spoon (or pipe) the cheese filling into each cooled manicotti shell. Arrange the filled shells in the baking dish.
Top: Pour the remaining sauce over the filled pasta. Make sure the shells are completely covered so they do not dry out.
Bake: Cover the dish tightly with foil. Bake for 40 minutes until the sauce is bubbling.
Broil: Remove the foil. Move the oven rack to the highest position and turn on the broiler. Sprinkle the top with the remaining 1 cup Parmesan and ½ cup mozzarella. Broil for 2 to 4 minutes. Watch it closely to ensure the cheese melts and browns lightly without burning.
Serve: Let the manicotti rest for 15 minutes. Garnish with fresh herbs and serve.

A collage showing the finishing steps: the baked pasta sprinkled with shredded cheese, the fully broiled golden-brown casserole, and a spatula lifting a serving out of the pan.

Top Recipe Tips

Slightly undercook the manicotti so they hold their shape during filling and baking.
Cover the pasta fully with sauce to prevent dry edges.
Let the baked manicotti rest before serving so the filling sets cleanly and slices easily.

High Altitude Adjustments

At elevations above 5,000 feet, reduce the oven temperature to 365°F and check for doneness a few minutes earlier. The filling may set faster, so avoid overbaking once the center is hot and the sauce is bubbling.