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Home » Recipes » Pasta

Gluten-free Cheesy Baked Pasta

Modified: Aug 22, 2025 by Meeta Arora · Leave a Comment

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Cheesy Baked Pasta in a white plate

Make this easy and delicious gluten-free cheesy baked pasta because pasta night doesn't have to be boring.

Don't get me wrong; my kids love it when I make simple spaghetti with a gluten-free spaghetti sauce. Sometimes, though, you just want to make something a little more special. That is when I make this gluten-free pasta bake because it makes any pasta night a thousand times better. Don't worry it's just as easy to make.

Overhead look of baking dish with a serving of a gluten-free cheesy pasta bake cut out next to a bowl of salad.
Jump to:
  • Ingredients.
  • Ingredient substitutions.
  • How to make gluten-free baked pasta.
  • Tips and tricks.
  • Storing.
  • Make gluten-free baked pasta ahead of time.
  • More gluten-free pasta recipes to enjoy.
  • 📖 Recipe

Ingredients.

This gluten-free pasta bake tastes like spaghetti and lasagna had a baby. It is SO good but beyond easy to make with only a few ingredients.

  • Gluten-free Pasta
  • Ground Beef
  • Gluten-free Marinara Sauce
  • Onions
  • Mushrooms
  • Sour Cream
  • Cream Cheese
  • Butter
  • Mozzarella Cheese
  • Parmesan Cheese
  • Spices
Overhead view of the ingredients needed to make a cheesy gluten-free baked pasta dish.

Ingredient substitutions.

  • Gluten-free pasta. - If you don't want to use gluten-free pasta, you can easily use cooked and shredded spaghetti squash instead. I have also used the palm heart noodles in this gluten-free pasta bake, and they worked great and kept their texture in this dish. That will also make this a low-carb pasta dish.
  • Gluten-free spaghetti sauce - You can use whatever brand of gluten-free spaghetti sauce that you like in this cheesy pasta bake. When I want to add more veggies to this gluten-free pasta bake, I will use a batch of my vegetable marinara.
  • Ground beef - You can also use ground turkey or chicken instead of ground beef if you prefer.
  • Vegetarian pasta bake. - If you want to make this gluten-free baked pasta vegetarian, you can simply by leaving the ground meat out of the sauce.

How to make gluten-free baked pasta.

Step 1. Cook your gluten-free pasta of choice and set it aside.

Step 2. Make the layers.

This gluten-free baked pasta consists of layers of creamy, cheesy covered pasta, gluten-free marinara, and more cheese. Which is why I say it's like spaghetti and lasagna had a baby.

  1. Mix the cream cheese, butter, sour cream, and half the parmesan into a small bowl.
  2. Make the gluten-free pasta sauce layer with the ground beef and veggies.
  3. Toss the cooked gluten-free pasta into the cream cheese mixture to coat the pasta.
Overhead view of the different steps for making the layers for a gluten-free baked pasta.

Step 3. Assemble the gluten-free pasta bake to go into the oven.

  1. Layer some of the sauce into the bottom of a casserole dish.
  2. Add a layer of the pasta, then some of the shredded mozzarella and parmesan.
  3. Then add another layer of the sauce.
  4. Repeat with more pasta and cheeses.
  5. Then the remaining sauce.
  6. Top the gluten-free pasta bake with the remaining cheeses and pop it into the oven until the sauce is bubbly and the cheeses have melted.
Overhead view of the different layers being added to a casserole dish to make a gluten-free baked pasta dish.

Tips and tricks.

  • Bring your cream cheese and butter to room temperature. This simple step will make it easier to toss the spaghetti squash with it.
  • Don't overcook your pasta. - Because this gluten-free baked pasta uses already cooked pasta to assemble it, you want to make sure you only cook your gluten-free pasta till it's almost done and not all the way done. If you cook it all the way, your gluten-free pasta can become soggy since it is cooked more in the sauce.

Storing.

Store leftovers of this gluten-free baked pasta dish in a container in the fridge for no more than four to five days. If you want to store it longer than that, then I suggest freezing it.

Make gluten-free baked pasta ahead of time.

I make this gluten-free baked pasta dish ahead of time a lot.

  • You can make and assemble it, place it in the fridge and then bake it off when you are ready to eat. It can be stored in the fridge for 2-3 days before baking.
  • You can even assemble and freeze this gluten-free casserole to have on hand and bake it off later. You can freeze it for up to two months.

Pro tips for freezing this gluten-free baked pasta dish.

  • I did notice when using spaghetti squash, it held onto some more liquid. I recommend making sure your sauce is a little bit thicker, or you can add an egg or two to the cream cheese mixture to help it stay thicker if you are going to freeze it.
  • Use a freezer-safe container or even a disposable one if you are going to freeze this gluten-free casserole. If you are using a glass or ceramic, make sure you let it fully defrost and the dish sits at room temperature before placing it in the oven. Placing a cold dish in a hot oven can cause it to crack.
  • If you are using a disposable baking pan from frozen, there is no need to defrost it before baking. Just add an additional 10-15 minutes to the baking time.

More gluten-free pasta recipes to enjoy.

  • Overhead view of a scoop of a gluten-free chicken casserole being taken out of a baking dish.
    Gluten-free Baked Chicken Parmesan Casserole
  • Buffalo Ranch Chicken Casserole
    Buffalo Ranch Chicken Casserole
  • Up close view of homemade gluten-free pasta sauce being served over spaghetti noodles in a bowl.
    Gluten-free Marinara Pasta Sauce
  • Cold pasta salad in a bowl ready to be the best side dish at your next gathering.
    Quick and Easy Pasta Salad with Chicken - Gluten-free
Looking towards a plate with a serving of gluten-free baked spaghetti next to a casserole dish.

📖 Recipe

Up close look at a slice of gluten-free spaghetti bake on a plate with a fork.

Gluten-free Cheesy Baked Pasta

Meeta Arora
Make this easy and delicious gluten-free cheesy baked pasta because pasta night doesn't have to be boring.
5 from 1 vote
Print Recipe Pin Recipe
Prep Time 15 minutes mins
Cook Time 45 minutes mins
Total Time 1 hour hr
Course beef, Main Course, pasta
Cuisine Italian
Servings 8
Calories 547 kcal

Ingredients
  

  • 1 Pound Ground Beef or ground meat of choice
  • 1 Package Gluten-free Spaghetti Spaghetti squash or other gluten-free pasta of choice.
  • 1 Cup Sliced Mushrooms
  • 1 Small Diced Onion
  • 1 28 OZ Jar Marinara Sauce of Choice
  • 2 Tablespoons Butter
  • ½ Cup Sour Cream
  • 8 Ounces Cream Cheese
  • 1 Cup Parmesan Cheese Divided
  • 2-3 Cups Mozzarella Cheese Shredded
  • 2 Teaspoons Salt
  • 1 ½ Teaspoons Pepper
  • 2 Cloves Minced Garlic Or 1 teaspoon garlic powder.
  • 2 ½ Teaspoons Italian Seasoning

Instructions
 

  • Cook and drain your gluten-free pasta, spaghetti squash, or other gluten-free pasta of choice, and set it aside.
    1 Package Gluten-free Spaghetti
  • In a skillet, cook and drain the ground beef.
    1 Pound Ground Beef
  • Add the diced onions and mushrooms to the ground beef and cook them until they become soft.
    1 Small Diced Onion, 1 Cup Sliced Mushrooms
  • Add the marinara sauce and spices and put it aside.
    1 28 OZ Jar Marinara Sauce, 2 Teaspoons Salt, 1 ½ Teaspoons Pepper, 2 ½ Teaspoons Italian Seasoning, 2 Cloves Minced Garlic
  • Combine the butter, cream cheese, sour cream, and half the parmesan cheese into a small bowl and mix.
    2 Tablespoons Butter, ½ Cup Sour Cream, 8 Ounces Cream Cheese, 1 Cup Parmesan Cheese
  • Toss the cooked spaghetti into the cream cheese mixture.
  • Preheat your oven to 350 degrees.
  • Layer a small amount of the marinara sauce into the bottom of a casserole dish.
  • Then put a layer of the coated spaghetti.
  • Top with a layer of mozzarella and parmesan.
    1 Cup Parmesan Cheese, 2-3 Cups Mozzarella Cheese
  • Add another layer of the marinara sauce.
  • Repeat until the baking dish is filled, and sprinkle the remaining cheese on top.
    2-3 Cups Mozzarella Cheese, 1 Cup Parmesan Cheese
  • Bake in the preheated oven for about 30-45 minutes or until the cheese bubbles and gets slightly golden.
  • Allow it to cool for a few minutes before serving and enjoy!

Notes

Ingredient substitutions.
  • Gluten-free pasta. - If you don't want to use gluten-free pasta, you can easily use cooked and shredded spaghetti squash instead. I have also used the palm heart noodles in this gluten-free pasta bake, and they worked great and kept their texture in this dish. That will also make this a low-carb pasta dish.
  • Gluten-free spaghetti sauce - You can use whatever brand of gluten-free spaghetti sauce that you like in this cheesy pasta bake. When I want to add more veggies to this gluten-free pasta bake, I will use a batch of my vegetable marinara.
  • Ground beef - You can also use ground turkey or chicken instead of ground beef if you prefer.
  • Vegetarian pasta bake. - If you want to make this gluten-free baked pasta vegetarian, you can simply leave the ground meat out of the sauce.
Tips and tricks.
  • Bring your cream cheese and butter to room temperature. This simple step will make it easier to toss the spaghetti squash with it.
  • Don't overcook your pasta. - Because this gluten-free baked pasta uses already cooked pasta to assemble it, you want to make sure you only cook your gluten-free pasta till it's almost done and not all the way done. If you cook it all the way, your gluten-free pasta can become soggy since it is cooked more in the sauce.

Nutrition

Calories: 547kcal
Keyword gluten free baked pasta, gluten free casserole, gluten free marinara sauce, gluten free pasta bake, gluten free spaghetti
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Meeta Arora, writer at Grain Free Table

Welcome to Grain Free Table! I’m Meeta- a busy wife, mom of two girls, and lover of food. Here you’ll find lots of easy and delicious gluten & allergy-friendly recipes, info about my favorite food & products, for a gluten-free way of life!

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