NEW RECIPE: Spaghetti Squash Bolognese Bake

I love a recipe that has all the things in one dish. This Spaghetti Squash Bolognese checks all the boxes: meat, cheese, veg, savory, filling, hearty…

I sub an entire jar of Eat Happy Kitchen Tomato Basil Marinara in place of the cans of tomatoes and tomato paste, and it takes the flavor of this dish to the next level. If you do this substitution, you can reduce the amount of overall salt added to the dish by a teaspoon.

You are welcome to sub in any veggie you like in place of the Brussels sprouts.

Y’all know I hate writing anything that’s not a recipe, so let’s get to the main event, shall we?

Spaghetti Squash Bolognese Bake

5 from 6 votes
Course Main Dishes
Cuisine Keto, Low Carb, NSNG


  • 1 spaghetti squash
  • 1 tablespoon olive oil
  • 1 medium onion, diced
  • 3 baby carrots, grated (about 1/4 cup of grated carrot)
  • 1 pound ground beef
  • 2 teaspoons salt
  • 1/2 teaspoon garlic powder
  • 1/2 teaspoon onion powder
  • 1/2 teaspoon white ground pepper
  • 1/2 teaspoon dried oregano
  • 1/2 teaspoon dried thyme
  • 7-10 basil leaves, chopped
  • 2 14-ounce jars canned diced tomatoes
  • 2 tablespoons tomato paste
  • 1/2 pound Brussels sprouts, ends trimmed and discarded, quartered
  • 1/4 cup heavy cream
  • 1 cup grated fontina cheese, divided
  • 1/3 cup grated fresh parmesan


  • Preheat oven to 350 degrees. Microwave spaghetti squash for 2 minutes to soften it. With a sharp, large kitchen knife, carefully cut spaghetti squash lengthwise into halves. Scoop out and discard seeds. Place squash halves face down on a foil lined baking sheet and cook until squash softly indents when you press it, about 40-45 minutes. Remove from heat and let cool. Scrape spaghetti strands out of squash with a fork into a medium mixing bowl, discarding shell. It should yield 2-3 cups.
  • Heat olive oil in a large, flat-bottomed sauté pan to medium high heat, until oil is shimmering. Add onion and carrot, and let soften, about 2-4 minutes. Add ground beef, and separate with spatula to bite sized pieces. Cook 5-6 minutes until beef is browned. Drain off excess grease. Add 1 teaspoon of the salt, the garlic powder, onion powder, white pepper, oregano, and thyme, and stir to mix spices with meat. Add chopped fresh basil and stir to soften basil, about 1 minute. Add canned tomatoes and tomato paste, stirring to mix in with meat. Add Brussels sprouts and mix in well. Stir in 1 remaining teaspoon salt. Bring sauce to a boil and then reduce heat to simmer to let sprouts soften, about 12-14 minutes. Remove from heat. Stir in heavy cream.
  • Pat dry any excess water from spaghetti squash strands. Fold in spaghetti squash evenly with meat and sprouts. Fold in 1/2 cup of the grated fontina cheese.
  • Pour contents of pan into a 9x12 casserole pan or Pyrex dish and flatten. Sprinkle remaining 1/2 cup grated fontina and the parmesan on top. Bake in oven 20-30 minutes, or until casserole and cheese are bubbling and starting to brown but not burn. Remove from oven, let stand 5-10 minutes, and serve.


  • NOTES:
  • In place of the canned tomatoes and tomato paste, you can use one jar of Eat Happy Marinara! If you use a jar of pre-made marinara, reduce the salt by a teaspoon.
  • Prepare the meat mixture while the spaghetti squash is baking in the oven to minimize overall cook time.
  • Make sure the spaghetti squash and the Brussels sprouts get soft enough while cooking. If veggies need more time, that's okay!
Keyword celiac, gluten free, keto, low carb, nsng, sugar free
Tried this recipe?Let us know how it was!


  • Marjorie Chesney / Reply

    5 stars
    Tried this recipe and loved it👍🏻 My husband doesn’t like spaghetti squash, but he’s not NSNG so I said fine. More for me. 🥰

  • 5 stars
    I love this so freakin’ much.

    This was only my second time cooking (or eating) spaghetti squash … and while cutting it open was a b***h, the results? Oh my ….

    • I know about cutting the squash, both hubby and I hacked at it for a while before I came up with Plan B as follows! Place the spaghetti squash in the microwave briefly to make it easier to cut, or ask the produce department of your grocery store to cut it in half for you, they will usually be glad to do so.

  • 5 stars
    This is such a great recipe! I am not a big fan of Brussel sprouts but I still loved this recipe. It’s also easily adaptable, you can substitute turkey, another vegetable for the Brussel sprouts, more or less cheese. Such a perfect fall or winter meal. It also reheats beautifully.

  • Misty Byers / Reply

    5 stars
    This is delicious! I used the Eat Happy marinara and followed the recipe exactly and it was perfect! I’ve tried other spaghetti squash/marinara bakes that were too heavy. This one will go into my “make it again” file for sure!

  • Elaine Wagg / Reply

    5 stars
    We both loved this! I used ground turkey and then I couldn’t find brussel sprouts (I admit I didn’t look too hard) so I used cauliflower and it was YUMMY! Now I’m searching for more recipes on this site.

    • Cauliflower is a perfect substitute! And yes, please keep searching for more recipes–I’m glad you’re here, and I hope you enjoy. I don’t post a recipe unless I’ve tested it multiple times and stand behind it 100%!

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