Cheese Manicotti Bake Recipe

If you’re craving a cozy, cheesy Italian dinner that feels like a warm hug, you’re going to love this Cheese Manicotti Bake Recipe. I absolutely love how this dish layers creamy ricotta, melty mozzarella, and sharp parmesan together inside tender pasta shells, all smothered in rich marinara sauce. When I first tried this recipe, it immediately became a family favorite because it’s both comforting and impressive enough for guests. Stick with me here—I’ll share all my best tips so you’ll have a flawless, mouthwatering meal every time!

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Why You’ll Love This Recipe

  • Creamy, Cheesy Goodness: This recipe combines ricotta, mozzarella, and parmesan for incredible flavor and texture.
  • Simple Prep, Big Impact: You’ll find the steps straightforward, but the result feels fancy and homemade.
  • Perfect for Entertaining: It’s a wonderful dish to make ahead and serve when friends or family drop by.
  • Comfort Food Classic: Everyone from kids to adults loves this warm, saucy pasta favorite.

Ingredients You’ll Need

Every ingredient here plays a role in creating layers of flavor and richness. I always recommend using fresh basil and good-quality cheeses—you’ll taste the difference, and your perfect Cheese Manicotti Bake Recipe will really shine.

  • Manicotti shells: Look for pasta that’s sturdy enough to hold the filling without breaking.
  • Olive oil: Keep it handy for preventing pasta from sticking and adding a subtle fruity note.
  • Ricotta cheese: Use whole milk ricotta if possible for creamier texture.
  • Garlic cloves: Minced or grated fresh garlic is best for aromatic depth.
  • Mozzarella cheese: Shredded mozzarella melts beautifully and creates that signature stretchy cheese pull.
  • Parmesan cheese: Freshly grated makes a huge difference in flavor over pre-grated.
  • Fresh basil: Adds a fragrant and vibrant note to lighten the richness.
  • Salt and pepper: Essential seasonings to bring every component together.
  • Ground nutmeg: Just a pinch brightens the ricotta filling in a surprising way.
  • Large eggs: Help bind the filling for easy stuffing.
  • Marinara sauce: Use your favorite homemade or store-bought sauce—homemade is my go-to whenever I can!
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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.

Variations

I love making this Cheese Manicotti Bake Recipe my own by swapping up the herbs or cheeses depending on what I have on hand. You should feel free to customize it to your taste, whether that’s adding a little heat or making it more veggie-packed.

  • Spinach or kale: I sometimes stir in sautéed spinach for extra greens and a dose of nutrients—my family doesn’t even notice!
  • Italian sausage: Adding cooked, crumbled sausage takes this dish from vegetarian to hearty meat-lovers’ delight.
  • Herb switch-up: Try fresh oregano or parsley in place of basil for a new twist on flavor.
  • Gluten-free pasta shells: Great if you’re avoiding gluten; just handle with care as they tend to be more fragile.

How to Make Cheese Manicotti Bake Recipe

Step 1: Prepare Your Pasta Shells

Start by boiling a large pot of salted water and cooking your manicotti shells for 6 to 7 minutes until they’re just al dente. You don’t want to overcook here because they’ll finish cooking in the oven and you don’t want mushy shells. Once drained, toss them gently with a tablespoon of olive oil to keep them from sticking while you work on your filling. I discovered this little tip saves lots of headaches—no broken manicotti shells in the dish!

Step 2: Whip Up the Cheese Filling

In a large bowl, combine ricotta, 2 cups shredded mozzarella, half the parmesan, minced garlic, chopped fresh basil, salt, pepper, and that secret ingredient—ground nutmeg. The nutmeg gives the cheese a subtle warmth that you might not expect but will appreciate. Whisk your eggs in a small dish, then gently fold them in so the filling binds nicely. Avoid over-mixing to keep it light and fluffy.

Step 3: Assemble Your Manicotti

Spread about 1½ cups of marinara sauce in the bottom of a 13×9-inch baking dish. Then, filling half the filling into a plastic bag, snip the corner, and pipe it carefully into each shell—one at a time. This method is way less messy than spooning filling in. Arrange each filled tube snugly in the dish over the sauce, then repeat with the remaining shells and filling. Pour the rest of your marinara sauce over the top for that lovely saucy finish.

Step 4: Bake to Perfection

Cover the dish with foil lightly coated in non-stick spray (so the cheese doesn’t stick), and bake at 350°F for 20 minutes. Then, take off the foil and bake another 10 to 15 minutes until everything bubbles and smells irresistible. Just before serving, sprinkle the remaining mozzarella and parmesan cheese over the top and pop it back in for 5 more minutes until the cheese melts into a golden, bubbly crown. Garnish with fresh basil, and voila—dinner is served!

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Pro Tips for Making Cheese Manicotti Bake Recipe

  • Don’t Overcook Pasta: Manicotti should be slightly undercooked before stuffing to avoid mushy texture after baking.
  • Use a Piping Bag: Filling the shells with a zip-top bag and snipped corner makes assembly neater and faster.
  • Oil Pasta to Prevent Sticking: Toss shells with olive oil once drained to keep them smooth and easy to fill.
  • Let It Rest Before Serving: Letting the bake sit for 5 minutes after coming out of the oven helps everything set and makes slicing clean.

How to Serve Cheese Manicotti Bake Recipe

The image shows two large pasta rolls placed on a pool of bright red tomato sauce on a white round plate, with a sprinkle of grated white cheese and small chopped green herbs on top. The pasta has a light yellow color and a textured surface with ridges, filled with a creamy white cheese mixture visible at the ends of the rolls. On the side of the plate, there is a small fresh salad made of green leafy lettuce, spinach, and a slice of red tomato. A silver fork is placed on the left side of the plate, resting on the white marbled surface. Photo taken with an iphone --ar 4:5 --v 7

Garnishes

I always finish with a sprinkle of chopped fresh basil—it adds freshness and keeps the dish bright. Sometimes I’ll add a drizzle of good-quality extra virgin olive oil or a few red pepper flakes for a little kick. A little grated parmesan on top just before serving doesn’t hurt, either.

Side Dishes

This goes beautifully with a crisp green salad—think arugula with lemon vinaigrette—or roasted vegetables like asparagus or broccoli. Garlic bread or a crunchy baguette rounds out the meal perfectly to scoop up any extra sauce.

Creative Ways to Present

For special occasions, I’ve baked individual manicotti in mini casserole dishes or even in large mushroom caps for a fun appetizer twist. Layering extra cheese between shells or topping with fresh herbs like thyme or oregano also makes it feel extra festive.

Make Ahead and Storage

Storing Leftovers

I store leftover cheese manicotti tightly covered in the fridge for up to 3 days. When reheating, I add a sprinkle of water or marinara sauce on top and cover loosely with foil in the oven to keep the pasta moist.

Freezing

I’ve frozen the whole assembled dish before baking by wrapping it tightly in plastic wrap and foil. When ready to bake, I thaw overnight in the fridge and follow the baking instructions, adding extra time as needed. It freezes beautifully without losing flavor.

Reheating

For best results, reheat leftovers in an oven preheated to 350°F covered with foil for about 20 minutes. This keeps the pasta from drying out and restores that bubbly baked-cheese goodness. Avoid microwaving if you can—it tends to dry things out unevenly.

FAQs

  1. Can I use no-boil pasta instead of manicotti shells?

    You can try no-boil tubes designed for stuffing, but traditional manicotti shells are easier to handle and hold stuffing better for this recipe. If you use no-boil, follow the package instructions carefully to avoid under or overcooking.

  2. Is there a way to make this dish ahead of time?

    Absolutely! You can assemble the stuffed manicotti and keep it covered in the fridge for up to 24 hours before baking. Just add a bit of extra sauce on top before baking to keep it moist.

  3. How do I prevent the manicotti from breaking?

    Be gentle when filling the shells and avoid overcooking them initially. Tossing cooked shells with a little olive oil helps prevent sticking and tearing.

  4. Can I substitute other cheeses in the filling?

    Yes! While ricotta, mozzarella, and parmesan are classic, feel free to mix in cottage cheese, fontina, or even goat cheese for different flavors and textures.

  5. What sauce pairs best with this Cheese Manicotti Bake Recipe?

    I recommend a classic marinara sauce, either homemade or a good-quality jarred variety. The acidity balances the richness of the cheese perfectly without overpowering it.

Final Thoughts

This Cheese Manicotti Bake Recipe has become my go-to for cozy nights and family gatherings alike because it’s both reliably delicious and surprisingly easy. It’s one of those dishes where you get all the comfort food vibes without the fuss, and you can tailor it to your tastes or what’s in your fridge. Trust me when I say that once you try baking these cheesy pasta tubes, you’ll find yourself making them again and again. So go ahead, give this recipe a shot—you’re going to impress yourself and anyone lucky enough to dive in!

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Cheese Manicotti Bake Recipe

Cheese Manicotti Bake Recipe

4.7 from 65 reviews
  • Author: Emily
  • Prep Time: 30 min
  • Cook Time: 40 min
  • Total Time: 70 min
  • Yield: 7 servings 1x
  • Category: Main Course
  • Method: Baking
  • Cuisine: Italian-American

Description

Delicious Three Cheese Manicotti is a classic Italian-American baked pasta dish featuring pasta shells stuffed with a rich mixture of ricotta, mozzarella, and parmesan cheeses combined with fresh basil and aromatic spices, all smothered in marinara sauce and baked to bubbly perfection.


Ingredients

Scale

Pasta

  • 1 (8 ounce) box manicotti shells (14 pasta shells)
  • 1 tablespoon olive oil

Cheese Filling

  • 32 ounces ricotta cheese
  • 4 garlic cloves (minced or grated)
  • 2½ cups shredded mozzarella cheese (9 ounces)
  • 1 cup grated parmesan cheese (divided, 4 ounces)
  • ½ cup chopped fresh basil
  • ½ teaspoon salt
  • ¼ teaspoon ground black pepper
  • ¼ teaspoon ground nutmeg
  • 2 large eggs

For Baking

  • 3 cups marinara sauce (24 ounces, homemade or store bought)
  • Non-stick oil spray for baking dish and foil


Instructions

  1. Preheat Oven: Preheat the oven to 350°F. Coat a 13 by 9 inch baking dish with non-stick oil spray and set aside.
  2. Cook Pasta Shells: Bring a large pot of salted water to a boil and cook the manicotti pasta shells for 6 to 7 minutes, until al dente. Drain, then return to the pot with a drizzle of olive oil to prevent sticking. Let cool while preparing the filling.
  3. Prepare Cheese Filling: In a large bowl, combine ricotta, 2 cups of mozzarella, ½ cup Parmesan, minced garlic, chopped basil, salt, pepper, and nutmeg. Whisk the eggs in a small dish and gently mix them into the cheese mixture until just combined.
  4. Prepare Baking Dish: Spread 1½ cups of marinara sauce evenly on the bottom of the prepared baking dish.
  5. Fill Manicotti Shells: Scoop half of the cheese filling into a plastic food bag and snip off a corner. Pipe the filling carefully into one pasta tube at a time. Arrange each filled tube in the baking dish on top of the marinara sauce. Repeat with remaining pasta shells and filling.
  6. Add Remaining Sauce and Cover: Pour the remaining marinara sauce over the filled pasta tubes. Spray a piece of foil with non-stick oil spray, cover the baking dish with it, and place in the oven.
  7. Bake Covered: Bake the dish covered for 20 minutes.
  8. Bake Uncovered: Remove the foil and continue baking for another 10 to 15 minutes until the sauce is hot and bubbly.
  9. Add Cheese Topping: Remove the dish from the oven and sprinkle the remaining mozzarella and Parmesan cheese evenly over the top.
  10. Final Bake: Return the dish to the oven and bake for 5 minutes or until the cheese melts and becomes slightly golden.
  11. Garnish and Serve: Remove from oven and garnish with additional chopped fresh basil. Serve hot.

Notes

  • This three cheese manicotti recipe combines ricotta, mozzarella, and Parmesan cheeses with fresh basil for a flavorful filling.
  • Using non-stick spray on both the baking dish and foil prevents sticking during baking.
  • Allow pasta shells to cool slightly before filling to prevent tearing and easier handling.
  • Snipping the corner of a plastic bag to pipe the filling makes stuffing the shells mess-free and efficient.
  • If you prefer a spicier dish, add red pepper flakes to the marinara sauce or cheese mixture.
  • Leftovers can be stored covered in the refrigerator for up to 3 days and reheated in the oven or microwave.

Nutrition

  • Serving Size: 1 manicotti shell
  • Calories: 281 kcal
  • Sugar: 3 g
  • Sodium: 611 mg
  • Fat: 16 g
  • Saturated Fat: 9 g
  • Unsaturated Fat: 6 g
  • Trans Fat: 0.002 g
  • Carbohydrates: 18 g
  • Fiber: 1 g
  • Protein: 17 g
  • Cholesterol: 74 mg