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Baked Manicotti with Homemade Sauce

Three-Cheese Manicotti

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Cheesy, saucy, and perfectly cozy! This three-cheese manicotti recipe wraps ricotta, mozzarella, and parmesan in tender pasta shells, baked with marinara.

If you’re wondering what’s bubbling in the oven that smells like a warm hug, it’s this three-cheese manicotti. It’s every bit as comforting as it sounds: tender pasta tubes, creamy ricotta filling, and a marinara situation that practically sings. When the cheese puffs up and the edges crisp just so, you’ll know you’re in for something good. It’s kind of the pasta version of slipping into fuzzy socks. Great for a cozy night in, a Sunday dinner you actually look forward to, or even meal prep if you’re thinking ahead (look at you being responsible). And let’s be honest, cheese-baked anything is never the wrong answer.

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Three-Cheese Manicotti

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Why You’ll Love this Three-Cheese Manicotti

No theatrics here, just honest-to-goodness pasta comfort. It’s cheesy, yes. But it’s also easy, satisfying, and weekend-supper worthy.

  • Creamy, savory filling: Ricotta and mozzarella mingle like old friends, tucked into every noodle like a secret.
  • No boiling needed: That’s right. The shells cook right in the oven. Less mess, fewer pots, more yay.
  • Bakes up bubbly and golden: The top gets that irresistible crispy-cheesy thing going on.
  • Leftovers? Even better: The flavors cozy up overnight and taste even more amazing the next day.
  • Easy to customize: Swap sauces, cheeses, or even sneak in greens (shh, they won’t know).
  • That tomato-cheese smell: You’ll know it when you smell it. The good kind. The deeply ‘someone’s cooking something amazing’ smell.

Three-Cheese Manicotti

Ingredient Notes

Not a long shopping list, which we love. Just a few star players doing what they do best.

  • Manicotti shells: These are the big tubes, not to be confused with cannelloni. No need to pre-cook them here, which is my favorite part.
  • Ricotta cheese: Whole milk ricotta gives you the most luscious result. If it seems very wet, it’s okay to drain it a bit.
  • Mozzarella cheese: Shredded and generous. It melts beautifully into the filling and forms that oozy top layer.
  • Parmesan cheese: Adds depth and sharpness. Save the good stuff for the topping, but pre-grated works just fine mixed in.
  • Eggs: They help bind the filling so it holds together as it bakes. You don’t notice them, but you’d miss them if they were gone.
  • Dried parsley: Just a touch for color and light herby flavor. Totally optional, but I like that little speckled green in the filling.
  • Marinara sauce: Grab your favorite jarred sauce or make it homemade if you’re feeling extra. Either way, the sauce sets the vibe here.
  • Water: Mixing water with the sauce helps cook the uncooked shells as they bake under foil—trust the process.

Three-Cheese Manicotti

How To Make This Three-Cheese Manicotti

This is a “pour yourself a glass of something and take it easy” kind of recipe. It smells good while it bakes and feels oddly therapeutic to pipe things into tiny tubes. Ready?

  • Preheat and prep: Set your oven to 350°F (175°C) and grab a 9×13-inch baking dish. Spray that baby with cooking spray and set it aside.

  • Water down the sauce: In a bowl, stir together your marinara and water. It’ll look a little soupy, which is exactly the point. Pour half into the dish to make a lovely sauce bed.

  • Make the cheese filling: In a separate bowl (I know, more bowls, but it’s worth it), mix the ricotta, half the mozzarella, ½ cup of the parmesan, both eggs, parsley, salt, and pepper. Give it a good stir until it looks creamy and fluffy.

  • Stuff the shells: Transfer that filling into a large zip-top bag and snip the tip—or use a piping bag if you’re fancy. Carefully squeeze the filling into each uncooked manicotti shell. Mildly satisfying, mildly messy, deeply worth it.

  • Nestle and sauce again: Lay the filled shells over the marinara in the dish. Keep them snug but not squished. Pour the rest of the marinara-water mix over the top.

  • Cover and bake: Foil tightly, pop in the oven, and bake for 50 minutes. The shells need that steam to cook through, so don’t peek. You’re not sneaking a look at presents here.

  • Uncover and cheese it: Pull off the foil, sprinkle on the remaining mozzarella and parmesan, and return to the oven for 10–15 more minutes. Watch for the top to bubble and get golden.

  • Let it rest: Wait 5–10 minutes before serving. It helps the cheese settle and gives you burn-free forks.

Three-Cheese Manicotti

Storage Options

Alright, maybe you made too much. Maybe you’re secretly hoping for leftovers. Either way, here’s how to keep this manicotti situation working in your favor.

Fridge storage is super simple. Just cover the baking dish with foil or transfer leftovers to a container with a tight-fitting lid. It’ll last up to 4 days. The sauce keeps the pasta nice and soft without going weird or dry.

Freezer? Yes, double yes. Assemble the manicotti ahead but stop before baking. Wrap the dish tightly in plastic wrap and foil (double up, trust me). Freeze for up to 2 months. When ready to bake, thaw overnight in the fridge and bake as normal. Or bake straight from frozen, just add 20–30 minutes extra time and cover with foil until gooey.

To reheat, a microwave works in a pinch but the oven is your best bet. Cover with foil and warm at 350°F until heated through—about 20 minutes if it’s a small portion, longer for a full pan.

Variations and Substitutions

Feel like switching it up? Good news: manicotti is surprisingly chill about that.

  • Spinach: Stir in a cup of thawed and squeezed-dry frozen spinach to the cheese filling for a pop of green and an extra excuse to eat more.
  • Meaty version: Mix cooked ground beef or Italian sausage into the sauce layer for serious hearty vibes.
  • Gluten-free pasta: Look for gluten-free manicotti or use large gluten-free shells. They’ll need a little extra sauce and maybe a few extra minutes to soften.
  • Alfredo sauce: Swap half (or all) of the marinara for Alfredo if you’re on a creamy kick. It’s wildly rich but also wildly awesome.
  • Different cheeses: Go wild! Try fontina, provolone, or a dollop of goat cheese mixed into the filling for a tangy twist.

Three-Cheese Manicotti

What to Serve with Three-Cheese Manicotti

This is definitely a main character dish, but a few clever sides can elevate the whole meal without stealing the spotlight.

  • A big leafy salad with a zippy vinaigrette cuts through all that creamy-cheesy richness like a champ. Bitter greens like arugula or radicchio are especially good here.

  • Garlic bread or soft dinner rolls make great sauce-sopping tools. No one’s judging bread-on-pasta choices here. Carb harmony is real.

  • Roasted broccoli or broccolini adds color, crunch, and that slightly charred thing that pairs perfectly with melty baked cheese. I like it with just olive oil and sea salt.

  • Feeling fancy? A little protein on the side, like this pan-seared salmon in pomegranate reduction, makes it look like you tried very hard (even if you didn’t).

  • And for dessert, something nostalgic but special, like homemade Tagalong cookies. Trust me, nobody’s mad about it.

Three-Cheese Manicotti

Pin it now, cook it later!

Don’t let this one slip away — pin it now and thank yourself later!

Pin It Now!

Pin it now, cook it later!

Don’t let this one slip away — pin it now and thank yourself later!

Pin It Now!

Frequently Asked Questions

Can I use no-boil manicotti shells?

Actually, this recipe assumes you’re using regular dry manicotti shells—no boiling needed because they soften in the oven thanks to that saucy bath. No-boil versions can work too, but check the package; they sometimes cook faster or may get too mushy. Just be sure the shells are fully covered in sauce before baking for best results.

How do I keep the filling from spilling out while stuffing?

That’s where the zip-top or piping bag method comes in clutch. Cut a reasonably small opening in the corner and gently squeeze from one end of the noodle while supporting the other. If the shell cracks a bit, just patch it together inside the dish—it’ll still bake up melty and wonderful. Nobody’s inspecting the insides.

Can I make this manicotti ahead of time?

Yes, definitely. Assemble the whole dish (stuff, layer, sauce) and store it tightly covered in the fridge for up to 24 hours before baking. It might need a few extra minutes in the oven if it’s cold from the fridge. Or assemble and freeze the whole thing for a future “I don’t feel like cooking” evening.

My sauce looks too watery—did I mess up?

Not at all. That watered-down marinara is working overtime here. It steams the pasta from the inside out, cooking the shells right in the dish. Once baked, most of the liquid gets absorbed, and what’s left just keeps everything nice and juicy. It’s like magic, but saucy.

Three-Cheese Manicotti

Three-Cheese Manicotti

Prep Time 25 minutes
Cook Time 1 hour 5 minutes
Total Time 1 hour 30 minutes
Cheesy, saucy, and perfectly cozy! Tender manicotti tubes are stuffed with a dreamy mix of ricotta, mozzarella, and parmesan, then baked with marinara until gorgeously golden and bubbly. All the joy of baked pasta, no pre-boiling required.
6 servings

Ingredients

Main Ingredients

  • 12 manicotti shells uncooked
  • 2 cups (450 g) ricotta cheese whole milk preferred; drain if watery
  • 2 cups (200 g) mozzarella cheese shredded, divided
  • 1 cup (90 g) parmesan cheese grated, divided
  • 2 eggs large
  • 1 tbsp dried parsley optional
  • 1 tsp kosher salt
  • 1/2 tsp (0.5 tsp) black pepper
  • 3 cups (700 ml) marinara sauce store-bought or homemade
  • 1/2 cup (120 ml) water

Equipment

  • 9x13 inch Baking Dish
  • Mixing bowls
  • Aluminum foil
  • Piping Bag or Zip-top Bag

Instructions
 

  1. Preheat your oven to 350°F (175°C) and spray a 9x13-inch baking dish with cooking spray.
  2. In a bowl, combine marinara sauce and water. Pour half of this mixture into your baking dish to coat the bottom.
  3. In a separate bowl, mix together ricotta, 1 cup mozzarella, 1/2 cup parmesan, eggs, dried parsley, salt, and pepper until smooth.
  4. Transfer the filling to a piping bag or a large zip-top bag with the corner snipped off.
  5. Pipe cheese filling into each uncooked manicotti shell, filling fully but gently.
  6. Place the stuffed shells in a single layer in the prepared baking dish over the sauce.
  7. Pour the remaining marinara-water mixture evenly over the shells.
  8. Cover the baking dish tightly with aluminum foil and bake for 50 minutes.
  9. Remove the foil, sprinkle the remaining mozzarella (1 cup) and remaining parmesan (1/2 cup) over the top.
  10. Bake uncovered for 10–15 minutes, until the cheese is golden and bubbling.
  11. Let rest for 5–10 minutes before serving.

Notes

For a pop of color and nutrients, stir thawed and squeezed-dry frozen spinach into the filling. The filling can be made ahead and refrigerated. To freeze: assemble but do not bake, cover tightly, and freeze for up to 2 months. Bake from thawed or add 20–30 minutes to bake time if cooking from frozen.

Nutrition

Calories: 440kcal | Carbohydrates: 37g | Protein: 25g | Fat: 22g | Saturated Fat: 13g | Cholesterol: 110mg | Sodium: 1160mg | Potassium: 410mg | Fiber: 3g | Sugar: 7g | Vitamin A: 830IU | Vitamin C: 6mg | Calcium: 590mg | Iron: 2.3mg

If you try this recipe, please leave a comment and rating below. I love to hear from you and always appreciate your feedback!

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So glad you stopped by Kitchenette Blog. I’m a line cook who’s completely obsessed with food—making it, eating it, and yep… chatting way too much about it. This little blog is where I share my favorite recipes, kitchen wins (and the occasional flop), and all the cozy, delicious things that make life tastier. Pull up a chair, we’re gonna eat well around here!

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