You’ll never even miss the traditional pasta with this amazingly delicious spaghetti squash spaghetti bake recipe! We fight over the leftovers, it’s so good.

I know using spaghetti squash in place of traditional pasta for good ol’ spaghetti is nothing new, but this spaghetti squash spaghetti bake (very redundant title alert) is extra delicious thanks to the fast and flavorful homemade sauce. I mean, the melty, glorious cheese on top doesn’t hurt anything, however that savory, delicious sauce is what steals the show.

Scoop of Spaghetti squash spaghetti bake topped with cheese in pan.

I’ve been on the fence about whether I would ever post this recipe, but seriously, after making it at least five times since early January (and serving it to several sets of company with very high reviews including the phrase “Mel, this is probably the most delicious thing you’ve ever fed me”), I decided for my own personal recipe sake, I wanted this spaghetti squash spaghetti to have a placeholder here on the blog. 

Scoop of Spaghetti squash spaghetti bake topped with cheese on a white plate.

I’ve long been a fan of spaghetti squash; I sometimes use it as a substitute for pasta or rice when I want a lower carb dinner. I cook it up and then ladle my portion of sauce/stroganoff/gravy over spaghetti squash while most of my family goes to town on the pasta or rice (except my vegetable loving 13-year old who gladly joins me in spaghetti squash land).

But for this recipe, I wanted to make an actual everyone-will-eat-this-together-or-else spaghetti bake that throws spaghetti squash into the forefront. And I don’t know why, but it’s just a million percent better mixed together and baked like this than spooning the same sauce over spaghetti squash has ever been.

The first time I made this, my 14-year old said, mid-bite, “wow, these noodles are so good,” and then surprisingly didn’t bat an eye when his younger sister destroyed his pasta hopes and dreams by excitedly telling him it was actually spaghetti squash. He just gave her a quick side eye (intuitively knowing she was trying to ruin his life) and dished up seconds. 

Close up of a forkful of spaghetti squash spaghetti bake topped with cheese on a white plate.

The components of the recipe are simple:

1) super quick weeknight homemade spaghetti sauce – not a whole lot more work than opening a jar of pasta sauce, this homemade version has incredible flavor. It’s so, so good and is what makes this spaghetti squash spaghetti bake really amazing, in my opinion.

2) spaghetti squash – if cooking it seems intimidating or foreign, never fear! I’m giving some tips below.

3) cheese – and lots of it. Or not. It’s your choice. Parmesan and mozzarella are both welcome here. 

Cut spaghetti squash with seeds.

There are two foolproof ways to cook spaghetti squash. First, in the Instant Pot. If you have one, it’s high time you threw some spaghetti squash in there. I have a post detailing how to cook spaghetti squash in the Instant Pot here, but in short, cut the spaghetti squash in half, scoop out the seeds, pour in 1 cup of water to the IP, add the rack and the squash, and cook on high pressure for 7 minutes. Perfecto. 

The second way is to cook the squash in the oven. I use this method particularly if I’m cooking more squash than will fit in the IP. I cut the spaghetti squash in half, scoop out the seeds, place the spaghetti squash cut side down on a lightly greased baking sheet (no water needed) and bake at 375 degrees for 40-50 minutes until it is very tender. 

After scraping the strands out of the squash, I like to let them sit for 5-7 minutes. Excess liquid/water will pool at the bottom of the strands, and draining that off will help the spaghetti squash bake not be too liquidy. But it’s totally optional (and the spaghetti is delicious either way). 

Spaghetti squash spaghetti bake topped with cheese in pan.

Anyway, there you have it. Spaghetti squash spaghetti bake. It’s so, so good. Just this weekend I made it for a family of seven visiting us (who incidentally are eating processed sugar- and gluten-free right now so it was the perfect meal; we subbed in honey for the brown sugar and coconut aminos for the soy sauce). I doubled it figuring we would have leftovers  coming out of our ears…but we all gobbled up every last bite. 

If you start with an oven safe pan (for making the sauce), you can toss the spaghetti squash in there and bake it in the same pan which will save you a dish to wash. Otherwise, you can transfer everything to a casserole/baking dish. I use an All-clad 4-quart cook/serve pan that was gifted to me years ago for everything (making the sauce and baking); this is the well-reviewed Cook’s Standard (much cheaper) alternative {aff. link} if you are looking for a similar pan.

I just used up the last of my spaghetti squash from my garden last summer (I kept it in a cool, dry spot in my pantry and it lasted forever); thankfully spaghetti squash is pretty easy to find in grocery stores even at this time of year so I can keep making this until my own garden pulls through for me later this year. 

One Year Ago: Pull-Apart Cheesy Pepperoni Pizza Sliders
Two Years Ago: Turkey and Swiss Sloppy Joes {30-Minute Meal}
Three Years Ago: German Pancake {Whole Grain Option} with Butter Syrup
Four Years Ago: Chocolate Covered Strawberries Tuxedo-Style
Five Years Ago: Cinnamon and Sugar Breadstick Twists

Scoop of Spaghetti squash spaghetti bake topped with cheese on a white plate.

Easy Spaghetti Squash Spaghetti Bake

4.88 stars (78 ratings)


  • 1 pound ground beef or ground turkey, (CAN LEAVE OUT FOR MEATLESS DISH)
  • ½ cup chopped onion
  • 2 cloves garlic, finely minced or 1/2 teaspoon garlic powder
  • 2 tablespoons tomato paste
  • 1 teaspoon dried basil
  • 1 teaspoon dried oregano
  • ¼ teaspoon dried thyme
  • ½ teaspoon coarse, kosher salt
  • ¼ teaspoon black pepper
  • 1 (28-ounce) can crushed tomatoes
  • 1 (8-ounce) can tomato sauce
  • 1-2 teaspoons brown sugar or honey
  • 1 tablespoon low-sodium soy sauce
  • 6 cups cooked spaghetti squash, (about 680-708) grams, about 2 small-medium squashes or 1 large drained of any excess liquid/water (see note)
  • 1 to 2 cups shredded mozzarella cheese
  • ½ cup shredded Parmesan cheese


  • Preheat the oven to 400 degrees F.
  • In a large 12-inch nonstick skillet (see note) over medium-high heat, cook the ground meat, onion, garlic, and a pinch of salt and pepper, breaking the meat into small pieces as it cooks, until the meat is not longer pink. Drain any excess grease.
  • Stir in the tomato paste, basil, oregano, thyme, salt and pepper. Cook over medium-high heat, stirring constantly, for about a minute, until the mixture smells fragrant.
  • Add the crushed tomatoes, tomato sauce, brown sugar and soy sauce. Stir to combine.
  • Bring the sauce to a simmer and cook for 5 minutes.
  • Add the cooked spaghetti squash noodles to the skillet (if it’s big enough; if not, transfer the sauce and spaghetti squash to a baking dish) and toss/stir to evenly combine. Pat the mixture into a somewhat even layer. Sprinkle with the mozzarella and Parmesan cheeses.
  • Bake for 20 minutes until the cheese and spaghetti are bubbling. Let rest for 10-15 minutes out of the oven before serving (the longer it rests, the less liquidy it will be).


Spaghetti Squash: this recipe calls for cooked spaghetti squash “noodles” – I usually use my Instant Pot for this following these instructions. You can also cook the spaghetti squash in the oven. Halve the spaghetti squash lengthwise, scoop out the seeds and place the squash face down or up on a baking sheet. Bake at 375 degrees for 40-50 minutes until tender. Let cool slightly before scraping up the strands of spaghetti squash.
Skillet: a 12-inch skillet isn’t large enough for the sauce and the spaghetti squash together, so you will need to transfer to an ovenproof baking dish to bake. If you have a larger skillet or a 3- or 4-inch deep pan that’s ovenproof, make the sauce in that so you can use it in the oven, too (and save transferring to another dish).
Servings: this recipe feeds our family of seven (a few of the younger kids are small eaters) with a few servings of leftovers. The recipe can definitely be cut in half (if so, it will fit just fine in a 12-inch skillet, so if the skillet is ovenproof, you can save a dish and bake it in there, too). But, the leftovers are also AMAZING (and individual portions would probably freeze great) if you want to make the full recipe.
Pasta: if you have a brand of pasta sauce you love and it comes in a 32-ounce jar, you could sub it in for the homemade sauce (and either leave the spaghetti squash amount the same or decrease slightly for a saucier dish).
Serving: 1 Serving, Calories: 369kcal, Carbohydrates: 21g, Protein: 24g, Fat: 22g, Saturated Fat: 10g, Cholesterol: 74mg, Sodium: 1324mg, Fiber: 5g, Sugar: 12g

Recipe Source: from Mel’s Kitchen Cafe (inspired from a recipe a MKC reader, Ashley, told me about – I used my weeknight spaghetti sauce with the spaghetti squash and nixed the eggs)