Three-Cheese Manicotti with Homemade Tomato Sauce

This Three Cheese Manicotti is filled with a creamy ricotta mixture, topped with melted mozzarella and Parmesan, and baked in a bright homemade tomato-basil sauce. It’s a comforting family dinner that’s ready in a little over an hour.

Baked Manicotti with Ricotta and Mozzarella

There’s something irresistible about a bubbling casserole fresh from the oven. This baked Three Cheese Manicotti uses large pasta tubes filled with a rich blend of ricotta, mozzarella, and Parmesan. The homemade tomato sauce made from San Marzano-style tomatoes and garlic adds brightness that balances the rich filling. It’s equally at home on a weeknight table or served for a gathering.

Ingredients

• Manicotti Shells: One 8-oz package; cook according to package directions but avoid overcooking so they keep their shape.
• San Marzano-style Tomatoes: Two 28-oz cans of whole peeled tomatoes for a slightly sweet, low-acid sauce base.
• Ricotta Cheese: 3 cups part-skim ricotta for a creamy filling.
• Mozzarella & Parmesan: Shredded mozzarella and grated Parmesan for the filling and topping.
• Eggs: Two beaten eggs to bind the cheese filling.
• Fresh Herbs: Chopped basil and parsley for freshness and color.

How To Make Baked Three Cheese Manicotti

In summary: cook the pasta, make a quick tomato-basil sauce, mix the three-cheese filling, assemble in a baking dish, bake until bubbling, and finish under the broiler for a golden top.

Prep the Pasta and Oven

1. Boil: Cook the manicotti to al dente per package instructions. Drain and transfer the shells to wax paper or foil lightly sprayed with nonstick spray to cool so they are easy to fill.
2. Preheat: Position the oven rack in the middle and preheat to 375°F (190°C).

Make the Tomato Sauce

1. Pulse Tomatoes: Add one can of tomatoes with their juice to a food processor and pulse 3–4 times until coarsely chopped. Repeat with the second can so the sauce has some texture.
2. Sauté: Heat 2 tablespoons olive oil in a large saucepan over medium heat. Add 3 minced garlic cloves and ½ teaspoon red pepper flakes; cook about 1 minute until fragrant.
3. Simmer: Stir in the chopped tomatoes and ½ teaspoon salt. Bring to a simmer and cook about 15 minutes until slightly thickened. Stir in 2 tablespoons chopped fresh basil and adjust seasoning to taste.

Make the Filling

1. Mix: In a medium bowl combine 3 cups ricotta, 8 oz (about 2 cups) shredded mozzarella, 2 oz (about 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 evenly combined.

Assemble and Bake

1. Base Layer: Spread about 1½ cups of the tomato sauce evenly over the bottom of a 9×13-inch baking dish.
2. Fill: Spoon or pipe the cheese mixture into each cooled manicotti shell and arrange them in the dish.
   
3. Top: Pour the remaining sauce over the filled shells so they’re fully covered to prevent drying.
4. Bake: Cover tightly with foil and bake for 40 minutes, until the sauce is bubbling.
   
5. Broil: Remove the foil, move the oven rack to the highest position, and turn on the broiler. Sprinkle with the remaining 2 oz Parmesan and 2 oz mozzarella (about 1 cup and ½ cup respectively) and broil 2–4 minutes until the cheese is melted and lightly browned — watch closely to avoid burning.
6. Serve: Let the manicotti rest 15 minutes so the filling firms up. Garnish with fresh basil and parsley and serve with extra grated Parmesan if desired.

High Altitude Adjustments

Above about 5,000 feet, lower the oven temperature to 365°F and check for doneness a few minutes earlier; the filling can set more quickly at high altitude, so avoid overbaking once the center is hot and the sauce is bubbling.

Did you make this comfort food classic? We’d love to hear how it turned out — leave a star rating and a comment below.

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Baked Three Cheese Manicotti

By Jillian for Food Folks and Fun

Cozy baked manicotti stuffed with a creamy three-cheese ricotta filling and smothered in homemade tomato basil sauce — an irresistible comfort-dinner favorite.

Prep: 30 mins

Cook: 44 mins

Cooling Time: 15 mins

Total: 1 hr 29 mins

Servings: 8 people

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Equipment

• Large pot
• Slotted spoon
• Nonstick cooking spray
• Food processor or blender
• Large saucepan
• Wooden spoon or silicone spatula
• Medium mixing bowl
• Whisk
• 9×13-inch baking dish
• Measuring cups & spoons
• Knife
• Cutting board
• Spoon or piping bag

Ingredients

Pasta

• 8 oz package manicotti

Tomato Sauce

• 2 (28-ounce) cans San Marzano-style whole peeled tomatoes
• 2 tablespoons olive oil
• 3 medium garlic cloves, minced
• ½ teaspoon red pepper flakes
• Salt, to taste
• 2 tablespoons chopped fresh basil

Filling

• 3 cups part-skim ricotta cheese
• 8 ounces shredded mozzarella (about 2 cups)
• 2 ounces grated Parmesan (about 1 cup)
• 2 large eggs, lightly beaten
• 2 tablespoons chopped fresh basil
• 2 tablespoons chopped fresh parsley
• ¾ teaspoon salt
• ½ teaspoon ground black pepper

Topping

• 2 ounces grated Parmesan (about 1 cup)
• 2 ounces shredded mozzarella (about ½ cup)

For Serving

• Chopped fresh basil
• Chopped fresh parsley
• Additional grated Parmesan, optional

Instructions

Cook the pasta

• Cook the manicotti according to package instructions. Use a slotted spoon to transfer cooked shells to wax paper or foil lightly sprayed with nonstick spray and let cool.

Prep the oven

• Move the oven rack to the middle position and preheat the oven to 375°F (190°C).

Make the sauce

• Add one can of tomatoes with juice to a food processor and pulse 3–4 times until coarsely chopped. Repeat with the second can.
• Heat olive oil in a large saucepan over medium heat, add garlic and red pepper flakes, and cook about 1 minute until fragrant.
• Stir in the tomatoes and ½ teaspoon salt, bring to a simmer, and cook about 15 minutes until slightly thickened. Stir in fresh basil and adjust salt to taste.

Make the cheese filling

• In a medium bowl combine ricotta, mozzarella, Parmesan, eggs, basil, parsley, salt, and pepper. Mix until smooth and evenly blended.

Assemble

• Spread 1½ cups of sauce over the bottom of a 9×13-inch baking dish.
• Spoon or pipe the cheese filling into each cooled manicotti and arrange them in the dish.
• Pour the remaining sauce over the filled shells, making sure they are completely covered.

Bake and broil

• Cover the dish tightly with foil and bake 40 minutes until bubbling.
• Remove foil, move the rack to the highest position, and preheat the broiler.
• Sprinkle with the remaining Parmesan and mozzarella, then broil 2–4 minutes until the cheese is melted and lightly browned—watch carefully to prevent burning.

Cool and serve

• Let the manicotti rest 15 minutes before serving. Garnish with basil and parsley and add extra Parmesan if desired.

Notes

Storage & Freezing

• Refrigerator: Store leftovers in an airtight container for up to 4 days. Reheat in the microwave or a 350°F oven until warmed through.
• Freezer: Assemble the unbaked dish, cover tightly with plastic wrap and foil, and freeze up to 3 months. Thaw overnight in the refrigerator before baking; you may need to add a few minutes to the bake time.

Nutrition

Serving: 2manicotti, Calories: 483kcal, Carbohydrates: 37g, Protein: 29g, Fat: 25g

Nutrition information is automatically calculated and should be used as an approximation.

Additional Info

Course: Main Dish

Cuisine: American, Italian

Recipe FAQs

Can I make manicotti ahead of time?

Yes — assemble up to 24 hours ahead, cover tightly, and refrigerate until ready to bake.

What’s the easiest way to fill manicotti shells?

Put the filling into a Ziploc bag (corner snipped) or a piping bag and pipe it into the shells.

What can I serve with manicotti?

Serve it with a simple side salad, garlic bread, or roasted vegetables for a complete meal.

More Comfort Food

• Sloppy Joe Pasta
• Tomato Basil Pasta
• Cream Cheese Lasagna