Name: Cheese Manicotti with Flavorful Tomato Sauce Recipe
Prep time: 45 min
Cook time: 1 h
Total time: 1 h 45 min
Cuisine: Italian
Ingredients: 2 tablespoons extra-virgin olive oil; ½ cup yellow onion, finely chopped; 1 tablespoon minced garlic; 1 teaspoon dried Italian seasoning; ¼ cup tomato paste; 28 ounces crushed tomatoes; 14.5 ounces diced tomatoes, do not drain; 1 teaspoon kosher salt; ¼ teaspoon black pepper; 4 quarts water; 1 tablespoon kosher salt; 1 pound manicotti pasta; 2 cups whole-milk ricotta cheese; 2 cups shredded mozzarella cheese, divided; ½ cup grated parmesan cheese, plus more for garnish; 1 large egg; 1 tablespoon chopped Italian parsley, plus more for garnish; 1 tablespoon chopped basil, plus more for garnish; 1 teaspoon dried Italian seasoning; 1 teaspoon kosher salt; ½ teaspoon black pepper; ⅛ teaspoon ground nutmeg

Jump to Recipe· 4.6 from 55 reviews

If you’re craving a cozy, comforting Italian dinner that’s not only delicious but sure to impress, you’re going to love this Cheese Manicotti with Flavorful Tomato Sauce Recipe. It’s one of those dishes I turn to when I want to wow friends or just indulge in a cheesy, saucy hug of a meal. The mix of ricotta and mozzarella wrapped in pasta tubes bathed in a rich, homemade tomato sauce? Simply irresistible. Stick with me, and I’ll share exactly how I make mine from scratch, plus some of my little kitchen hacks to make it perfect every time.

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Why This Recipe Works

Perfectly Balanced Flavors: The creamy cheese filling and tangy tomato sauce complement each other beautifully without overpowering.
Simple, Fresh Ingredients: Using fresh herbs and quality cheeses brings an authentic taste with minimal fuss.
Make-Ahead Friendly: You can assemble it ahead of time, which makes weeknight dinners or entertaining a breeze.
Customized Comfort: Whether you like it lighter or loaded with cheese, this recipe is super adaptable to your tastes.

Cheese Manicotti with Flavorful Tomato Sauce, cheesy pasta bake, Italian manicotti recipe, homemade tomato sauce, baked cheese manicotti - The image shows a white rectangular baking dish filled with two rows of stuffed pasta shells, each covered with a layer of chunky red tomato sauce, melted white cheese, and sprinkled with fresh green herbs. The pasta shells are a pale yellow color with ridged edges visible beneath the sauce and cheese. Around the dish, on a white marbled surface, there are small bowls with green herbs and grated cheese, and some fresh red tomatoes on the vine. The overall look is warm and freshly baked with slight sauce splatters on the edge of the dish, photo taken with an iphone --ar 2:3 --v 7

Ingredients & Why They Work

The magic of this Cheese Manicotti with Flavorful Tomato Sauce Recipe lies in simple, quality ingredients. Each component plays a role— from the tangy crushed tomatoes to the creamy ricotta mixed with mozzarella and parmesan. Pick fresh herbs when you can, and don’t skimp on good olive oil—it truly makes a difference in the sauce’s flavor.

Cheese Manicotti with Flavorful Tomato Sauce, cheesy pasta bake, Italian manicotti recipe, homemade tomato sauce, baked cheese manicotti - Flat lay of a small white ceramic bowl of extra-virgin olive oil, a small white bowl filled with finely chopped yellow onion, a small white bowl with minced garlic, a small white bowl of dried Italian seasoning, a small white bowl of tomato paste, a small white bowl heaping with crushed tomatoes, a small white bowl of diced tomatoes with juices, a small white bowl of kosher salt, a small white bowl of black pepper, uncooked manicotti pasta tubes arranged neatly, a small white bowl with whole-milk ricotta cheese, a small white bowl with shredded mozzarella cheese, a small white bowl of grated parmesan cheese, one large brown egg with clean shell, a small white bowl of chopped Italian parsley, a small white bowl of chopped basil, and a small white bowl containing ground nutmeg, all ingredients fresh and natural, placed on a clean white marble surface, soft natural light, photo taken with an iPhone, professional food photography style, fresh ingredients, white ceramic bowls, no bottles, no duplicates, no utensils, no packaging --ar 2:3 --v 7 --p m7354615311229779997

Extra-virgin olive oil: Adds smooth richness and helps develop onion and garlic flavors.
Yellow onion: Offers natural sweetness that balances tomato acidity.
Garlic: For that savory, aromatic base that’s so classic in Italian sauces.
Dried Italian seasoning: A blend of herbs that enhances the sauce’s depth.
Tomato paste: Concentrated tomato flavor giving body and richness.
Crushed and diced tomatoes: The heart of your sauce—use good quality canned for best results.
Kosher salt and black pepper: Essential seasoning to bring out all flavors.
Manicotti pasta: Tubular shells perfect for stuffing with the cheese mix.
Ricotta cheese: Creamy and mild, it forms the filling’s base.
Mozzarella cheese: Adds melty, stretchy goodness; divided for filling and topping.
Parmesan cheese: Sharp and nutty punch that enhances the mixture and garnish.
Egg: Binds the cheese filling to keep it luscious yet firm.
Italian parsley and basil: Fresh herbs brighten the filling and final dish.
Ground nutmeg: A tiny pinch adds warm complexity to the cheese filling.

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Note: You’ll find the complete list of ingredients, along with their exact measurements, in the printable recipe card at the bottom of this post.

Make It Your Way

One of the things I love about this Cheese Manicotti with Flavorful Tomato Sauce Recipe is how it invites your personal touch. Whether you want to add a bit of spice or swap in some greens, this recipe handles tweaks effortlessly. Don’t hesitate to experiment to match your taste buds or what’s in season.

Meat Variation: I often brown Italian sausage before mixing into the tomato sauce for a richer, heartier flavor.
Vegetable Boost: Adding sautéed spinach or mushrooms inside the filling ups the nutrition and flavor.
Dairy-Free: Try replacing cheeses with vegan ricotta and mozzarella for a dairy-free version I know friends have enjoyed.
Herb Swap: Fresh oregano or thyme can replace basil or parsley for a slightly different herb profile that’s delicious too.

Step-by-Step: How I Make Cheese Manicotti with Flavorful Tomato Sauce Recipe

Step 1: Sauté Aromatics for Your Flavorful Tomato Sauce

Start by warming olive oil over medium heat in a large pan. Toss in finely chopped onions and minced garlic with dried Italian seasoning. Stir frequently until the onions soften—about 3 minutes. This slow flavor-building step is key. Then, stir in tomato paste and cook for another minute to deepen the sauce’s richness before adding your crushed and diced tomatoes. Let everything simmer gently for about 10 minutes, stirring occasionally so it doesn’t stick or burn, and season with salt and pepper. This homemade sauce never fails to fill the kitchen with the most inviting aroma.

Step 2: Cook Manicotti Pasta Perfectly

Bring a large pot of salted water to a rolling boil, then add your manicotti shells. Cook for about 8 to 9 minutes until they’re al dente—soft but still holding their shape. Don’t overcook or they’ll tear when you fill them later! Drain and rinse with cold water to stop cooking and make handling easier. Lay them out in a single layer on a sheet pan. This little step saved me from wrecking a batch once — trust me, patience here pays off.

Step 3: Whip Up That Dreamy Cheese Filling

In a bowl, mix ricotta, half the shredded mozzarella, parmesan, egg, chopped parsley and basil with Italian seasoning, salt, pepper, and just a pinch of nutmeg. The nutmeg is a subtle trick that takes this filling from good to wow. Combine everything until smooth and creamy. The egg helps the filling hold together as it bakes but doesn’t make it heavy—just right.

Step 4: Stuff Each Manicotti Shell

This part feels a little like piping frosting on a cake and it’s super satisfying. Spoon your cheese filling into a large zip-top bag and snip off a corner (or use a piping bag if you have one). Carefully fill each manicotti shell — about 10 shells total — making sure each tube is nicely packed but not bursting. Place the filled shells back on the sheet pan; it keeps things organized and makes assembling the casserole easier.

Step 5: Assemble and Bake Your Manicotti

In a 13×9 inch baking dish, spread half of your tomato sauce on the bottom. Then arrange the stuffed manicotti in a single layer. Pour the remaining sauce evenly over the top and sprinkle with the rest of your mozzarella. Cover with foil and bake at 400°F for 30 minutes. Remove foil and bake another 5 minutes so the cheese gets that gorgeous bubbly finish. Your kitchen will smell amazing, and that bubbling cheese is always a sign you did it right.

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Tips from My Kitchen

Don’t Overcook the Pasta: Manicotti should be slightly under al dente before stuffing to avoid breaking apart in the oven.
Use a Piping Bag: Filling the shells is way easier and less messy when you pipe the cheese filling—trust me, I’ve learned the hard way!
Simmer Your Sauce Slowly: Giving your tomato sauce enough time to cook develops a deeper flavor; don’t rush it.
Let It Rest Briefly: After baking, let the manicotti sit for 5 minutes—this helps it set up so it slices neatly.

How to Serve Cheese Manicotti with Flavorful Tomato Sauce Recipe

Garnishes

I always top my manicotti with freshly chopped parsley and basil right before serving. A sprinkle of extra parmesan cheese on top adds nuttiness and an elegant touch. These little pops of fresh herbs brighten the rich tomato sauce and creamy cheese filling. Sometimes, a little cracked black pepper over the top makes it even better!

Side Dishes

I love pairing this manicotti with a crisp green salad tossed in a simple vinaigrette to cut through the richness. Garlic bread or toasted bruschetta also complements it beautifully—nothing beats dipping warm crusty bread into that flavorful tomato sauce.

Creative Ways to Present

For special occasions, I sometimes arrange each manicotti on individual plates with a little extra sauce and garnish on the side, then drizzle with a balsamic glaze for a fancy touch. Another fun idea is layering the manicotti vertically in a casserole dish to create a stunning presentation that’s sure to impress your guests.

Make Ahead and Storage

Storing Leftovers

I usually store leftover manicotti in an airtight container in the fridge; it keeps well for up to 5 days. Make sure it’s cooled completely before sealing to avoid sogginess. Reheating works beautifully if you add a splash of water or extra sauce to keep it moist.

Freezing

This recipe freezes perfectly! I assemble the whole casserole but don’t bake it, then tightly cover with plastic wrap and foil. When you’re ready to eat, thaw overnight in the fridge and bake as usual, adding a bit more time since it’s cold. I’ve found freezing doesn’t compromise the pasta’s texture or the cheese filling’s creaminess.

Reheating

I warm leftovers covered in the oven at 350°F until bubbly, about 20 minutes, or microwave single servings with a damp paper towel over the top to keep moisture locked in. Avoid overcooking here to prevent the pasta from drying out.

FAQs

Can I use no-boil manicotti pasta for this recipe?

Absolutely! Using no-boil manicotti can save you some prep time. Just be sure to cover the baking dish tightly with foil and bake for a bit longer to let the pasta absorb the sauce and cook through properly.
What’s the best way to avoid tearing the manicotti shells when filling?

Start with pasta that’s slightly undercooked and cooled completely. Using a piping bag to fill the shells gently and evenly reduces pressure that might cause tearing. Also, don’t overfill—leave a little space to prevent breakage.
Can I make the tomato sauce ahead of time?

You sure can! Making the sauce a day or two in advance lets the flavors deepen even more. Store it in the fridge in a sealed container and reheat gently before assembling your manicotti.
What if I don’t have ricotta cheese?

You can substitute with cottage cheese blended smooth for a similar texture, though ricotta’s creaminess is ideal. Alternatively, mascarpone can make it extra rich but will alter the flavor slightly.
How do I make the Cheese Manicotti with Flavorful Tomato Sauce Recipe gluten-free?

Simply swap regular manicotti pasta with a gluten-free version that holds up well to boiling. Be sure to check cooking times as they can vary, and handle the pasta gently to avoid breaking.

Final Thoughts

This Cheese Manicotti with Flavorful Tomato Sauce Recipe holds a special place in my kitchen because it’s the perfect blend of comfort and elegance, all rolled into one. Whether you’re feeding family on a busy weeknight or entertaining friends, it’s a crowd-pleaser that never feels fussy. I’m excited for you to try it—make it your own, savor every bite, and enjoy all those ooey-gooey cheesy moments that make cooking truly joyful.