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Twice Baked Spaghetti Squash

I’ll be honest. The first time I had spaghetti squash, I was a little underwhelmed.

The texture is obviously not pasta, so I wasn’t expecting some kind of culinary miracle, but the squash “noodles” didn’t really absorb the flavor of the sauce.

It just sat on top like some (super) sad excuse for hippie spaghetti. Womp womp.

Mixing it with the sauce before plating didn’t really make it any better. I could rationalize eating it again if I thought of it like a vegetable, not a pasta replacement, but there are so many other tasty vegetables out there that I’d rather eat. (And if I’m gonna go for veggie noodles, zucchini seems to do a better job.)

I wrote off spaghetti squash as another one of those “meh” vegetables.

Then, my mom suggested I try twice baked spaghetti squash.

The gist? Roast a spaghetti squash per usual, but instead of scooping out the noodle-y flesh and topping with sauce, fill the baked squash with meat sauce, top with cheese, and put it BACK IN THE OVEN.

Baked that sucker TWICE.

I didn’t think that would do much, but boy was I wrong. When she made twice baked spaghetti squash during a recent visit, I finally healed my rocky relationship with spaghetti squash.

Seriously, if you’ve tried to love spaghetti squash in the past and weren’t impressed, give this twice baked method a shot before you write it off completely. I’m glad I did.

A heads up on my recipe for Twice Baked Spaghetti Squash: I multitask while I cook to get everything to the table as fast as possible.

That means:

  • I prep the squash and get it in the oven before doing anything else
  • While the squash is baking (for the first time), I prep the sauce and get the cheese ready
  • Then, I can quickly fill the squash with sauce, top with cheese, and let the oven work its final magic

Twice Baked Spaghetti Squash

  • 1 large spaghetti squash (I find organic spaghetti squash has way better flavor)
  • 2 Tbsp extra-virgin olive oil
  • 1 teaspoon salt
  • ½ cup water
  • 1 lb. hot Italian pork sausage, pasture-raised, if possible
  • 1 large onion, diced
  • ½ cup ish sliced mushrooms
  • 1 tsp dried oregano
  • 1 tsp garlic powder
  • ½ tsp black pepper
  • 1 jar high-quality marinara sauce or 3-4 cups homemade marinara
  • 12 oz mozzarella cheese, shredded (from grass-fed milk, if possible)
  • 6 oz Parmesan cheese, shredded (from grass-fed milk, if possible)


  1. Preheat oven to 400 degrees F.
  2. Slice the spaghetti squash in half lengthwise and scoop out the seeds. (Watch those fingers! Use a large, sharp knife. Reserve seeds and roast separately like pumpkin seeds.)
  3. Rub the inside of the squash with olive oil and sprinkle with salt.
  4. Place each squash half, cut side down, on large rimmed baking sheet, such as a lasagna pan. Add ½ cup water.
  5. Bake for 30-45 minutes, until the squash is tender. (It’s cooked when it gives slightly when you push on the outside or if the inside of the squash easily forks into spaghetti strands.)
  6. While the squash is cooking, prep the filling.
  7. In a large cast iron pan, cook the pork sausage, breaking it into chunks as it cooks. When enough fat has rendered, add the onions and mushrooms. Add oregano, garlic, and pepper. Continue to cook until onions are translucent and meat is cooked through.
  8. Add marinara sauce. Bring to simmer and remove from heat. Set aside.
  9. Once squash is cooked, remove from oven. Fill with sauce. Top with cheese. Return to oven on the top rack and make for 10-15 minutes, or until cheese is melted/browned to your liking.
  10. Let sit for 10 minutes (if you can wait!) to let the juices sink in.
  11. Serve by scooping the flesh of the squash with a large spoon. The squash should break apart into spaghetti-like strands while serving.

Recipe Notes

NOTE: I like to double the recipe and freeze the second squash for later. Simply bake the squash once, fill with marinara, top with cheese and let cool (do not bake twice - YET). Wrap with parchment paper, then foil (here’s why you don’t want foil directly touching tomato sauce!), and freeze for up to 2 months.

When ready to bake, remove from freezer the night before you plan to eat. Set in a baking dish in the fridge to defrost. The next day, unwrap the squash and bake at 400 degrees F for 35 minutes, or until sauce is heated and bubbling at the edges of the squash.

And there you have it: Twice Baked Spaghetti Squash that has amazing flavor and is a breeze to prep.

Last time I made this, I completely forgot that I was gonna take pictures for the blog, hence we already ate one half of the squash before I snapped a pic. Oops.

But, hey, that tells you how good it is. Family meals that look messy on the plate usually taste delicious.

Nonetheless, here is one messy lil’ pic from my plate before I gobbled up the whole thing.

Until next week,

PS – I hope this opens up a whole ‘nother world with spaghetti squash for you. After you try this recipe, play around with other fillings. For example, my friends over at The Real Food RDs have an amazing twice baked spaghetti squash with a buffalo chicken filling. YUM!

Veggies: Eat them because you want to, not because you have to

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Lily Nichols is a Registered Dietitian/Nutritionist, Certified Diabetes Educator, researcher, and author with a passion for evidence-based prenatal nutrition and exercise. Her work is known for being research-focused, thorough, and unapologetically critical of outdated dietary guidelines. She is the author of two bestselling books, Real Food for Pregnancy and Real Food for Gestational Diabetes.


Leave a comment
  1. I too have found spaghetti squash to be underwhelming. I look forward to trying this recipe! Thanks!

    • Yes! Baking spaghetti squash twice makes all the difference and really lets the flavors absorb into the “noodles.” Enjoy it, Courtney.

  2. How funny, I’m sitting on the counter and opened my email and started to read this while I literally have spaghetti squash roasting away in the oven. This sounds great- will definitely give it a try!! In the south, all sorts of squash grow abundantly, so we eat spaghetti squash often. Tonight is an antipasto chopped salad mixed with the squash and a basil-parsley pesto as the dressing. An easy go-to that’s uses a lot in the fridge. Can’t wait to try your recipe! Thanks, Lily!

    • Oooh nice. I bet a twice baked spaghetti squash with a pesto filling would be divine!

  3. Lily,
    I made this last night and it was a hit with our family – even the kids gobbled it up. Next time I may try adding a bag of frozen spinach (defrosted and squeezed of extra water) to add more veggies.

    I also was never a fan of spaghetti squash because it is so flavorless, but you’re right, twice baked spaghetti squash is a whole different animal.

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