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Home / Blog / Recipes

High Protein Baked Manicotti

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By:

Madeline

Published: April 24, 2025

This site may contain affiliate links. Please read my disclosure policy.

This High Protein Baked Manicotti is the perfect weeknight meal or meal prep option that everyone will love. It has all of the flavor of a classic baked manicotti with a few ingredient swaps to up the protein in each serving.

a three quarter view of baked manicotti in a casserole dish

Weeknight-easy

Make ahead

You’ll Learn: How to balance acidity and sweetness for a better tomato sauce

Worth It: It’s a satisfying, protein-forward option that actually keeps you full

Bonus: Comfort food that is ready to reheat

a three quarter view of baked manicotti in a casserole dish

Why You’ll Love This Recipe

  • Great for meal prep – This easy baked manicotti recipe with meat is great to have on hand for an easy lunch to reheat. Plus it makes the perfect comfort food.
  • Delicious high protein meal – Each serving has over 35 grams of protein to make sure you feel totally satisfied!
  • Easy to make – Most of the time spent on this recipe is cooking in the oven. It’s one of my favorite easy dinner ideas. You just need to brown your beef and stuff the noodles to bring this recipe together. It’s the perfect Italian food for a large crowd.
a close up photo of baked manicotti on a plate

Serving Suggestions

Because this baked manicotti is so high protein, I love to add a simple green on the side. You could make air fryer brussels sprouts or air fryer asparagus to keep it easy.

If you would like to make a simple salad to go with it, you could top it with green dream dressing or this balsamic vinaigrette. For a bit of bread to go with your cheesy pasta dishes, I love serving some garlic bread.

an above view photo of the ingredients for baked manicotti with labels on them

Ingredients

  • Manicotti noodles – the manicotti shells are the perfect tube shape pasta shell for your cheese filling
  • Cottage cheese – the cottage cheese adds creaminess and protein to your baked manicotti and takes the place of a typical ricotta filling
  • Ground beef – use browned ground beef to make your meat filling
  • Salt – a bit of salt intensifies all of the flavors in this manicotti pasta recipe
  • Italian seasoning – I used an Italian seasoning blend, but you could also create your own mixture of your favorite Italian herbs
  • Garlic powder – the garlic powder supplements the Italian seasoning for the best flavor in your stuffed manicotti
  • Marinara – use your favorite jarred spaghetti sauce or make homemade red sauce for this recipe
  • Shredded mozzarella cheese – you can use pre-shredded mozzarella or grate your own

Ingredient substitutions

In place of ground beef, you could use ground turkey, ground pork, or ground chicken, or Italian sausage. If you use a leaner meat like turkey, you may want to add a bit of extra-virgin olive oil to the pan when cooking.

The cottage cheese adds protein to your meat sauce, but you could also use different kinds of cheese. Ricotta cheese would be delicious in your cheesy filling.

Feel free to top your baked manicotti with extra cheese like quarter cup parmesan cheese, black pepper, red pepper flakes, and fresh herbs like fresh basil.

a photo of pasta tubes next to a photo of cottage cheese in a large mixing bowl

How to make

Step 1: Prepare Manicotti and Cottage Cheese

Pre heat oven to 350F and grease a casserole dish.

Over high heat, boil noodles in salted boiling water for 2 minutes less time than package directions for al dente instructs. Drain and set aside in a strainer or on paper towels (Image 1).

Blend cottage cheese until smooth and place in a large bowl (Image 2).

a photo of ground beef in a skillet next to a photo of cottage cheese and ground beef in a medium bowl with a spatula

Step 2: Brown the ground beef

Brown ground beef in a skillet over medium heat, drain any excess oil and season with teaspoon salt, Italian seasoning and garlic powder (Image 3). Allow to cool slightly before mixing with the blended cottage cheese (Image 4).

Pour a thin layer of the 1-2 cups sauce into the casserole dish and reserve the remaining marinara sauce. For the easiest way to fill the large tubes of pasta, use a large plastic bag or a piping bag to pipe the cheese and beef mixture into the bottom three-quarters of each noodle of cooked manicotti (Image 5).

a photo adding meat sauce from a ziploc bag to the top quarter of noodle with tomato sauce on the bottom of the pan next to a photo of the noodles covered in rest of the sauce sauce and shredded cheese

Step 2: Assemble the casserole

Arrange the filled manicotti in a single layer in the baking dish and top with the remaining marinara sauce. Sprinkle manicotti with the 1.5 cup of mozzarella cheese on top of the pasta sauce (Image 6) and cover manicotti with foil.

Bake covered on the oven rack in the middle position at 350F for 40 minutes. Remove the aluminum foil and bake for an additional 5-10 minutes to brown the cheese. If you would like it browned more, heat broiler and watch closely to avoid burning. Cook times can vary depending on your oven.

an above view photo of baked manicotti in a casserole dish

Storage and Freezing

Once prepared, allow the baked manicotti to cool completely and cover dish or transfer to an airtight container. Then, store the manicotti in an airtight container in the refrigerator for up to 4 days. It is delicious the next day.

To reheat next time, take the leftovers out of the fridge and reheat in an oven, toaster oven, or in microwave.

Check out these other Casserole Dish recipes

  • Stuffed Pepper Casserole
  • Sloppy Joe Casserole
  • Stuffed Shells with Meat
  • Baked Gnocchi Recipe

You can find the full recipe below. If you make this recipe, please rate and review it in the comments, or share it with me on Instagram!

You can find the full recipe below. If you make this recipe, please rate and review it in the comments, or share it with me on Instagram!

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a three quarter view of baked manicotti in a casserole dish

Recipe

High Protein Baked Manicotti

4.75 from 4 votes
This high protein baked manicotti is a perfect meal for the whole family.
Recipe By: Madeline
Prep: 15 minutes minutes
Cook: 45 minutes minutes
Print Review Pin It SaveSaved!
Servings: 6

Ingredients

  • 8 oz manicotti noodles
  • 2 cups cottage cheese
  • 1 lb lean ground beef
  • 1 tsp salt
  • 1 tsp italian seasoning
  • 1 tsp garlic powder
  • 24 oz marinara
  • 1.5 cups shredded mozzarella cheese
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Instructions

  • Preheat oven to 350F and grease a casserole dish.
  • Boil pasta in salted water for 2 minutes less than package directions instructs. Drain and set aside.
  • Blend cottage cheese until smooth and place in a large bowl.
  • Brown ground beef in a skillet over medium heat, drain any excess oil and season with salt, italian seasoning and garlic powder. Allow to cool slightly before mixing with the blended cottage cheese.
  • Pour a thin layer of the marinara sauce into the casserole dish. Use a large plastic bag or a piping bag to pipe the cheese and beef mixture into the cooked manicotti.
  • Arrange the filled manicotti in the casserole dish and top with the remaining marinara sauce. Top with the mozzarella cheese and cover the casserole dish with foil
  • Bake covered at 350F for 40 minutes. Remove the foil and bake for an additional 5-10 minutes to brown the cheese.

Nutrition Information

Calories: 426kcal (21%), Carbohydrates: 38g (13%), Protein: 37g (74%), Fat: 14g (22%), Saturated Fat: 7g (44%), Polyunsaturated Fat: 1g, Monounsaturated Fat: 4g, Trans Fat: 0.3g, Cholesterol: 81mg (27%), Sodium: 1374mg (60%), Potassium: 787mg (22%), Fiber: 3g (13%), Sugar: 7g (8%), Vitamin A: 784IU (16%), Vitamin C: 8mg (10%), Calcium: 236mg (24%), Iron: 4mg (22%)

This website provides approximate nutrition information for convenience and as a courtesy only. Nutrition data is gathered primarily from the USDA Food Composition Database, whenever available, or otherwise other online calculators.

Did you make my High Protein Baked Manicotti?

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Recipe Rating




7 responses

  1. Abby
    May 4, 2025

    4 stars
    It was good, but not sure I’m sold on the cottage cheese trend. My spouse said it was good, but he questioned what I did with the beef, as it with the cottage cheese made it an odd gray color. Not sure it’ll go in my rotation but definitely higher protein stuffed manicotti.

    Reply
  2. Karah McClain
    May 4, 2025

    5 stars
    Such an easy weeknight recipe packed with flavor!

    Reply
    1. Madeline
      May 5, 2025

      So happy you like it!

      Reply
  3. Christie
    May 5, 2025

    5 stars
    Good high protein & carb option to fuel my teens after a day of school and sports practices.

    Reply
    1. Madeline
      May 5, 2025

      Yay!!

      Reply
  4. Liz
    September 27, 2025

    5 stars
    Easy to follow directions! My 8 year old asked me to put it on our meal rotation!

    Reply
    1. Madeline
      September 29, 2025

      Awww, well that is a win in my book!

      Reply

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