This Three Cheese Manicotti is stuffed with creamy ricotta, mozzarella, and Parmesan, then baked in a homemade tomato-basil sauce for a comforting dinner.
Table of Contents
Baked Manicotti with Homemade Sauce
There is something deeply comforting about a bubbling pan of manicotti coming out of the oven. The edges are lightly golden, the sauce is rich with basil and garlic, and the filling is creamy and satisfying without feeling heavy. This Three Cheese Manicotti is the kind of dinner that feels special enough for company, yet simple enough for a weeknight when you want a classic baked pasta.
My recipe leans into technique and texture. The sauce is bright and balanced, the filling is well seasoned, and the final broil gives you that irresistible cheesy top that makes everyone ask for seconds.
Ingredients, Why They Mattter, and Cost
Per Serving Cost: $2.25
Recipe Cost: $18.02
These simple, classic ingredients each play an important role. Read for explanations, substitutions, and more.
Pasta
- Manicotti pasta (8-ounce package): These large pasta tubes are designed for stuffing and baking. Cook them just to al dente since they will continue cooking in the oven. If you slightly undercook them, they will hold their shape better and be easier to fill. You can substitute oven-ready manicotti if you prefer not to boil, though the texture will be slightly firmer.
Tomato Basil Sauce
- San Marzano Style Whole Peeled Tomatoes (two 28-ounce cans): Whole peeled tomatoes give you control over texture. A quick pulse in the food processor creates a rustic sauce that feels homemade. Use San Marzano tomatoes for a sweeter flavor, or crushed tomatoes for a smoother finish.
- Olive oil (2 tablespoons): Olive oil adds richness to the sauce. Extra virgin olive oil gives a deeper flavor, though regular olive oil works well too.
- Garlic (3 medium cloves, minced): Fresh garlic builds the foundation of the sauce. Cook just until fragrant to avoid bitterness. If you are sensitive to garlic, reduce to two cloves.
- Red pepper flakes (½ teaspoon): This adds subtle warmth. Adjust up or down depending on your preference.
- Salt (to taste): Salt brings out the tomato flavor. Start with the suggested amount and adjust after simmering.
- Fresh basil (2 tablespoons, chopped): Stirred in at the end for a fresh finish. Dried basil can be used in a pinch, though fresh makes a noticeable difference.
Three Cheese Filling
- Part-skim ricotta cheese (3 cups): Ricotta provides the creamy base. If your ricotta seems watery, drain it in a fine mesh strainer for 30 minutes before mixing. Whole milk ricotta can be used for a richer filling.
- Shredded mozzarella (8 ounces, about 2 cups): Mozzarella gives stretch and structure. Low-moisture mozzarella works best here.
- Grated Parmesan cheese (2 ounces, about 1 cup): Parmesan adds depth and saltiness. Freshly grated Parmesan melts more smoothly than pre-grated.
- Large eggs (2, lightly beaten): Eggs bind the filling so it slices cleanly after baking.
- Fresh basil (2 tablespoons, chopped): Adds brightness inside the filling.
- Fresh parsley (2 tablespoons, chopped): Parsley balances the richness of the cheeses.
Toppings
- Grated Parmesan (2 ounces, about 1 cup): Creates a lightly crisp, savory layer on top.
- Shredded mozzarella (2 ounces, about ½ cup): Melts into that classic cheesy blanket during broiling.
How To Make Three Cheese Manicotti
Cook the pasta, simmer a simple tomato-basil sauce, mix the three-cheese filling, stuff the manicotti, bake until bubbly, then broil for a golden, cheesy top.
Prep the Oven
- Adjust the oven rack to the middle position and preheat to 375°F.
Make the Tomato Basil Sauce
- Add one can of whole tomatoes with juices to a food processor. Pulse three to four times until coarsely chopped. Repeat with the second can.
- Heat olive oil in a large saucepan over medium heat. Add the garlic and red pepper flakes and cook for about one minute until fragrant.
- Stir in the tomatoes and ½ teaspoon salt. Bring to a gentle simmer and cook for about 15 minutes, stirring occasionally, until slightly thickened.
- Remove from the heat and stir in the chopped basil. Taste and adjust salt as needed.
Make the Three Cheese Filling
- In a medium bowl, combine the ricotta, mozzarella, Parmesan, eggs, basil, parsley, salt, and black pepper. Stir until evenly mixed.
- For easier filling, spoon the mixture into a large zip-top bag, then snip off one corner to pipe it into the pasta.
How To Stuff Manicotti:
- Spread 1½ cups of sauce across the bottom of a 9-by-13-inch baking dish.
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Transfer the cheese filling into a piping bag or a large Ziploc bag with the corner snipped off, and pipe the filling directly into each end. If you don’t have a bag, you can carefully use a small spoon or butter knife to fill the shells from both sides, pushing the mixture toward the center.
- Arrange them in a single layer in the dish.
Bake
- Pour the remaining sauce evenly over the pasta, covering the tops completely.
- Cover the dish tightly with foil and bake for 40 minutes until hot and bubbling.
Broil and Serve
- Remove the foil. Move the oven rack to the highest position and preheat the broiler.
- Sprinkle the Parmesan and mozzarella evenly over the top. Broil for 2 to 4 minutes, watching carefully, until the cheese is melted and lightly golden.
- Let the manicotti rest for 15 minutes before serving. Garnish with fresh basil, parsley, and extra Parmesan.
Top Tips for Perfect Manicotti
- Slightly undercook the pasta. This ensures it holds its shape during filling and baking.
- Drain ricotta if it appears watery to prevent a loose filling.
- Let the dish rest before slicing so the filling sets properly.
High Altitude Adjustments
At higher elevations, pasta dishes can dry out more quickly.
- Add 2 to 4 tablespoons of extra sauce over the top before baking.
- Cover tightly with foil to prevent moisture loss.
- Check for doneness about 5 minutes before the listed time.
Recipe and Flavor Variations:
- Beef and Cheese Manicotti: Brown 1 pound of ground beef and drain the grease. Mix the cooked beef into the cheese filling. Reduce the ricotta cheese to 15 ounces to accommodate the meat.
- Baked Manicotti Puttanesca: Sauté 3 minced anchovy fillets with the garlic when making the sauce. Stir ¼ cup of chopped Kalamata olives and 2 tablespoons of capers into the cheese filling.
- Baked Manicotti with Spinach: Thaw a 10-ounce package of frozen chopped spinach and squeeze it until completely dry. Mix the spinach and a pinch of nutmeg into the cheese filling, then stuff the shells.
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Three Cheese Manicotti
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This Three Cheese Manicotti is stuffed with creamy ricotta, mozzarella, and Parmesan, then baked in a homemade tomato-basil sauce for a comforting dinner.
Equipment
- large pot
- Food processor or Blender
- Large skillet or saucepan
- 9×13-inch baking dish
- large mixing bowl
- Piping bag or Ziploc bag
- Cheese grater
- aluminum foil
- spatula
- measuring cups and spoons
Ingredients
PASTA:
- 8 oz package manicotti
TOMATO SAUCE:
- 2 (28-ounce) cans Hunt’s San Marzano Style Whole Peeled Tomatoes
- 2 Tablespoons olive oil
- 3 medium cloves garlic minced
- ½ teaspoon red pepper flakes
- salt
- 2 Tablespoons chopped fresh basil
FILLING:
- 3 cups part-skim ricotta cheese
- 8 ounces shredded mozzarella cheese about 2 cups
- 2 ounces grated Parmesan cheese about 1 cup
- 2 large eggs lightly beaten
- 2 Tablespoons chopped fresh basil
- 2 Tablespoons chopped fresh parsley leaves
- ¾ teaspoon salt
- ½ teaspoon ground black pepper
TOPPING:
- 2 ounces grated Parmesan cheese about 1 cup
- 2 ounces shredded mozzarella cheese about ½ cup
FOR SERVING:
- Chopped fresh basil
- Chopped fresh parsley
- Grated Parmesan
Instructions
COOK PASTA:
- Cook pasta according to package instructions. Using a slotted spoon, transfer the boiled manicotti to cool on a piece of wax paper or foil that has been lightly sprayed with nonstick cooking spray.8 oz package manicotti
PREP OVEN:
- Move the oven rack to the middle position and preheat the oven to 375°F.
MAKE SAUCE:
- Pulse 1 can of tomatoes, with their juice, in a food processor until coarsely chopped, about 3 or 4 pulses. Transfer tomatoes to a bowl and repeat with the remaining can of tomatoes.2 (28-ounce) cans Hunt’s San Marzano Style Whole Peeled Tomatoes
- In a large saucepan over medium heat, add oil, garlic, and red pepper flakes. Heat until the garlic is fragrant, about 1 minute.2 Tablespoons olive oil, 3 medium cloves garlic, ½ teaspoon red pepper flakes
- Stir in tomatoes and ½ teaspoon of salt and bring the sauce to a simmer. Continue to simmer until the sauce is slightly thickened, about 15 minutes. Stir in fresh basil and season the sauce with salt.salt, 2 Tablespoons chopped fresh basil
MAKE CHEESE FILLING:
- In a medium bowl, stir together ricotta, 2 cups mozzarella, 1 cup of grated Parmesan, eggs, and salt and pepper. Combine ricotta, 1 cup Parmesan, mozzarella, eggs, basil, parsley, and salt and pepper.3 cups part-skim ricotta cheese, 8 ounces shredded mozzarella cheese, 2 ounces grated Parmesan cheese, 2 large eggs, 2 Tablespoons chopped fresh basil, 2 Tablespoons chopped fresh parsley leaves, ¾ teaspoon salt, ½ teaspoon ground black pepper
TO ASSEMBLE:
- In a 9×13-inch baking dish, spread 1 ½ cups of sauce on the bottom.
- Using a spoon, spoon the cheese filling into a cooled manicotti and arrange in baking dish. Repeat with remaining manicotti.
- Next, completely cover manicotti with remaining sauce.
BAKE AND BROIL:
- Cover baking dish with foil and bake for 40 minutes, or until bubbling.
- Remove baking dish from the oven, and adjust the oven rack to the highest position. Close oven and preheat the broiler.
- Top manicotti evenly with 1 cup of grated Parmesan cheese and ½ cup of shredded mozzarella cheese.2 ounces grated Parmesan cheese, 2 ounces shredded mozzarella cheese
- Place manicotti under the broiler and keep a watchful eye as the cheese broils for about 2-4 minutes. Remove the manicotti from the oven once the cheese is melted and is spotty brown.
- Cool manicotti for 15 minutes.
TO SERVE:
- Garnish with chopped fresh basil and parsley and serve with additional Parmesan cheese.Chopped fresh basil, Chopped fresh parsley, Grated Parmesan
Notes
- SERVE: You can keep the baked manicotti at room temperature for up to 2 hours before refrigeration is required.
- STORE: Cover with plastic wrap or foil and refrigerate for up to 2-3 days.
- FREEZE: Cover the baked and cooled dish in two layers of plastic wrap and two layers of foil, and freeze up to 2-3 months.
Nutrition
Serving: 2manicotti | Calories: 471kcal | Carbohydrates: 32g | Protein: 30g | Fat: 25g | Saturated Fat: 13g | Cholesterol: 122mg | Sodium: 939mg | Potassium: 439mg | Fiber: 2g | Sugar: 4g | Vitamin A: 1083IU | Vitamin C: 11mg | Calcium: 635mg | Iron: 2mg
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Recipe FAQs
What is the difference between cannelloni and manicotti?
The two are similar, and people often confuse them. However, it comes down to how each dish is made.
Cannelloni typically has meat and veggies, along with cheese, rolled inside the pasta.
Manicotti, on the other hand, is a pasta filled with just a cheese mixture. The sauce layered on top may have meat or veggies in it, though.
Can you make Baked Manicotti ahead of time?
Yes, you can make manicotti ahead of time and bake it later! You have two options.
Freezer Instructions: Prepare the recipe as directed, stopping before the Bake and Broil step. Cover the baking dish tightly with two layers of plastic wrap and two layers of foil. Freeze for up to 3 months.
To Bake from Frozen: Remove the plastic wrap and the top layer of foil. Bake covered for 2 hours or until heated through. Proceed with the broiling instructions as directed.
Can I use cottage cheese instead of ricotta?
Yes, blend full-fat cottage cheese until smooth for a similar texture.
What is the best way to fill manicotti?
Using a piping bag or zip-top bag makes the process quicker and less messy than spooning.
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Anything with three different types of cheese is a favorite of mine! So flavorful and delicious!
I absolutely LOVE Baked Manicotti and I never think to make it at home! I’ve never seen it look this good and it is absolutely going on our must-make dinner list 🙂 Can’t wait to try out that tomato sauce, too!
You had me at three cheese. This looks totally comforting.
Family favorite right here!! This is definitely a recipe to save and it does freeze well! Thanks for sharing all the tips.
One of my comfort food with three kind of cheeses. Sigh, I’m in love. 🙂
YUM! Cheese manicotti is a family favorite at our house. I’m really glad to see Hunt’s offering San Marzanos too!
This cheese manicotti is one of our favorite comfort foods. Pasta and cheese, what’s not to love? Yummy!!