This three cheese manicotti is made with manicotti noodles stuffed with mozzarella cheese, ricotta and Parmesan, covered with marinara, baked then topped with fresh basil!

Other baked pasta favorites include stuffed shells, baked mostaccioli and baked ziti!

Baked cheese manicotti in a baking dish.

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Cheese Manicotti

Three cheese manicotti is a baked pasta recipe that I like to think of as a hearty Italian-American casserole like my favorite million-dollar spaghetti recipe. It’s the ultimate comfort food served with garlic bread or easy breadsticks and chopped salad.

Thanks to my homemade marinara sauce and Italian seasoning blend this cheese manicotti is just as delicious as anything you’d find at your favorite Italian restaurant! Add it to your cozy meal rotation along with this eggplant Parmesan.

Recipe Ingredients

Cheese manicotti ingredients on marble counter.

Find the full printable recipe with specific measurements below.

  • Manicotti noodles: These are large tube-shaped noodles with ridges. Boil them as per package directions.
  • Mozzarella cheese: Use freshly grated mozzarella if you can. In other words, grate it yourself from a soft mozzarella ball or block.
  • Ricotta cheese: Whole milk ricotta is best to use, substitute with cottage cheese or goat cheese if that is what you have on hand.
  • Parmesan cheese: Freshly grated from a block.
  • Eggs: Two large help bind the ricotta filling.
  • Seasonings: Italian seasoning, salt and pepper.
  • Marinara sauce: I like to use a homemade sauce, but if you’re looking for an easier way I would suggest the Kirkland brand from Costco. Spaghetti sauce works, too.
  • Garnish: Fresh basil although other fresh herbs would be delicious, too!

Manicotti Variations

  • Three cheese manicotti with meat: As is this dish is vegetarian, if you would like you can add Italian sausage, ground beef, or shredded chicken.
  • Veggies: Mushrooms, onions, or chopped bell peppers add in more tender crunch and flavor.
  • Greens: Spinach is a great health benefit and adds a beautiful color to the cheese manicotti.
  • Seasonings: Onion powder, garlic powder, and nutmeg all bring in their own flavor and variation.
  • Herbs: Oregano, fresh parsley, or basil are unique and often used in Italian dishes.
  • Spicy: Make it spicy with a few red pepper flakes sprinkled overtop.

How to Make Three Cheese Manicotti

Add ricotta cheese, mozzarella, Parmesan, eggs, Italian seasoning, salt, and pepper to a large bowl then mix until combined. Transfer filling to a ziploc bag then snip one corner of the bag and squeeze filling inside cooked manicotti sheel.

Cheese, seasonings and ricotta with eggs in a bowl.
Ricotta filling in a bag being piped into a manicotti tube.

Spread 1/2 of the marinara sauce onto the baking dish and place the stuffed noodles on top of the sauce in an even layer. 

Pour any remaining sauce over the noodles and sprinkle with remaining cheese. Cover dish with foil and bake manicotti for 20 minutes. Remove foil and bake for 5-10 minutes more until cheese is bubbly. Rest for a few minutes then garnish with fresh basil!

Three cheese manicotti with marinara and basil on top.

Expert Tips

  • Stuffing the shells. If you don’t have any Ziploc bags or piping bags, you can spoon the filling into the manicotti pasta shellls. It’s just a little messier this way.
  • Cook the manicotti shells to al dente. They will continue to cook while baking, so you don’t want the manicotti overcooked.
  • Bring it to room temperature. If you’ve made this casserole dish ahead of time, take it out of the fridge and bring it to room temperature about 40 minutes before baking. 
Three cheese manicotti on a white plate.

Craving more classic pasta dishes? Try my carbonara pasta, spaghetti and meatballs or my favorite chicken alfredo recipe.

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Three cheese manicotti on a white plate.

Three Cheese Manicotti

5 from 11 votes
Recipe by: Jamielyn Nye
Prep Time: 20 minutes
Cook Time: 25 minutes
Total Time: 45 minutes
Servings: 8
This three cheese manicotti is made with tender tubes of manicotti stuffed with mozzarella cheese, ricotta and Parmesan, covered with marinara, baked then topped with fresh basil!
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Ingredients 

  • 10 ounces manicotti noodles
  • 3 cups ricotta cheese
  • 1 ½ cups grated fresh mozzarella cheese , divided
  • ¾ cup grated parmesan cheese , plus more if desired
  • 2 large eggs , beaten
  • 2 teaspoons Italian seasoning
  • ½ teaspoon Kosher salt
  • ¼ teaspoon ground black pepper
  • 24 ounces marinara
  • Chopped fresh basil

Instructions

  • Prep. Preheat the oven to 350°F. Spray a 9×13-inch baking dish with nonstick spray.
  • Cool noodles. Boil the manicotti noodles according to package directions.
  • Combine three cheese filling: In a large zip-top bag, add 3 cups ricotta, 1 cup mozzarella, 1/2 cup parmesan, 2 eggs, 2 teaspoons Italian seasoning, 1/2 teaspoon salt, and 1/4 teaspoon pepper. Mix together until combined.
  • Pipe filling into noodles. Snip one corner of the bag and pipe the filling inside the cooked noodles.
  • Assemble, cover and bake. Spread 1/2 of the marinara onto the bottom of the baking dish. Place the noodles on top of the sauce. Spread the remaining marinara over the top. and sprinkle with the remaining 1/2 cup mozzarella. Cover with foil and bake 20 minutes.
  • Rest then serve. Remove foil and bake an additional 5 to 10 minutes, or until the cheese is bubbly. Remove from oven and let sit a few minutes before serving. Top with fresh basil. Serve while hot.

Last step: Please leave a comment and rating after you make the recipe.

Notes

Make-ahead: This dish can be made 24 hours in advance before baking. You can also place in a foil pan and freeze until ready to bake (up to 3 months). 
Variation: This dish tastes great with 1 cup shredded chicken and/or 1 cup chopped spinach mixed in with the cheese mixture. 
Noodles: If you can’t find manicotta, you could also use cooked flat lasagna noodles. Simply place 1/4 cup filling on one end and roll up. 
Homemade marinara: Check out my homemade marinara recipe. I prefer Kirkland brand if I’m not making homemade. 

Nutrition

Calories: 434kcal, Carbohydrates: 36g, Protein: 25g, Fat: 21g, Saturated Fat: 12g, Polyunsaturated Fat: 1g, Monounsaturated Fat: 6g, Trans Fat: 0.01g, Cholesterol: 118mg, Sodium: 942mg, Potassium: 486mg, Fiber: 3g, Sugar: 5g, Vitamin A: 1078IU, Vitamin C: 6mg, Calcium: 415mg, Iron: 2mg

Nutrition provided is an estimate. It will vary based on specific ingredients used.

Recipe FAQs

How to serve 3 cheese manicotti?

Since this dish is saucy, cheesy, and a bit heavier, a crisp light salad is a great pairing. Salads like this wedge salad, Mediterranean quinoa salad, or an easy chopped salad. An easy ratatouille would also be great.

Can I make cheese stuffed manicotti in advance?

You can assemble it up to 2 days ahead of time and bake it when you’re ready. Or you can wrap it up and transfer it to an airtight container and keep it frozen for up to 3 months. Thaw in the fridge overnight or bake from frozen for an extra 10-15 minutes.

Can I freeze this three cheese manicotti recipe?

Yes, but before baking. Assemble it, cover it with plastic wrap then keep it frozen for up to 3 months. Thaw in the fridge overnight or bake from frozen adding an extra 10-15 minutes.