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    Home » Side Dishes » Twice Baked Spaghetti Squash

    Published: Mar 17, 2021 · Modified: Aug 17, 2021 by Carolyn

    Twice Baked Spaghetti Squash

    This post may contain Amazon or other affiliate links. As an Amazon Associate I earn from qualifying purchases.

    156.0K shares
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    This keto spaghetti squash is twice baked for a delicious melty, cheesy side dish. It’s easy to make and takes only 6 ingredients. And it’s baked right in the shells for less mess and less clean up!

    Titled image of twice baked spaghetti squash in the skin, in an oval dish. A fork is digging into it.

    I cook a lot of spaghetti squash over the fall and winter. It’s such a readily available squash and it’s so darn useful. Even if you’re not on a low carb or keto diet, spaghetti squash is such a great alternative to heavy pasta and it holds up well to sauces and toppings.

    My favorite treatment of spaghetti squash is really quite simpl: some butter, some garlic, some parmesan and a sprinkle of salt and pepper. It’s easy, it’s delicious and the leftovers make a great breakfast! Putting it back into the shells and baking it with some gooey, melty cheese on top makes for a mouthwatering presentation as well.

    And this baked spaghetti squash recipe is one of the easiest keto side dishes you will ever make. It ranks up there with my cauliflower mushroom risotto, and my creamy mashed cauliflower.

    It’s been a fan favorite for a long time, with good reason!

    A close up shot of a fork lifting cheesy baked spaghetti squash out of the shell.

    Is spaghetti squash keto?

    Spaghetti squash is extremely healthy and full of nutrients. It contains a whole host of important vitamins and minerals like Vitamin A, several B vitamins, magnesium, and potassium.

    And compared to many winter squash varieties, it’s quite low in carbs, coming in at only 7g of carbs per cup (101 grams).

    When it’s cooked with some healthy fats and seasonings, it makes an excellent keto side dish. You can also add some protein like chicken, sausage, or ground beef and turn it into a hearty keto dinner recipe.

    Two halves of a cooked spaghetti squash, filled with cheese, butter, and garlic, in an oval baking dish.

    Oven baked spaghetti squash

    There are any number of ways to cook spaghetti squash, all of them equally good. You can cook it in a slow cooker or instant pot, or you can simply bake it in the oven.

    It does need to be cut in half prior to being baked. You want a large, very sharp knife for this, and a good amount of pressure to slice through the thick skin. You can scoop the seeds out before baking or after, it really doesn’t matter. Bake until it’s soft enough to scoop out the stringy flesh easily.

    But be careful not to overcook it, as the strings tend to break up more and lose their resemblance to spaghetti noodles. When the outer shell is soft enough to squeeze and indent it, remove the spaghetti squash from the oven or the slow cooker.

    A collage of photos showing how to make twice baked keto spaghetti squash.

    How to make Twice Baked Spaghetti Squash

    This recipe is simple and straightforward, but results in the best keto spaghetti squash.

    You will need:

    • a large baking sheet
    • parchment paper
    • 1 medium spaghetti squash, about 3 to 4 lbs (or two small ones)
    • butter
    • garlic
    • dried basil or oregano
    • salt and pepper
    • sliced cheese that melts nicely (provolone or mozzarella)

    Cut the squash lengthwise

    Most recipes require you to cut across the squash, but lengthwise allows you to use the shells for the second baking. Use a very large sharp chef’s knife and get above the squash so you can use your weight to press down. I often place the whole cutting board right on the floor.

    Cut side down

    Place the squash cut-side down on the prepared baking sheet, so that the flesh isn’t exposed to the heat of the oven. This way, it won’t dry out as much during baking.

    Bake until squeezable

    The bake time depends on the size of the squash so check it frequently. You know it’s done when you can squeeze it and feel it give way to the pressure. Don’t bake it any longer.

    Scoop it out

    Scoop the flesh of the squash in to a bowl and stir in butter, Parmesan, garlic, and seasonings. Toss well to combine, then stuff the empty skins with this mixture.

    Add the cheese

    You want a good melty sliced cheese, like provolone or mozzarella, for extra scrumptiousness.

    Bake again

    The second baking takes only about 8 to 10 minutes, to melt the cheese.

    Top down image of keto spaghetti squash baked in the shell, topped with melted cheese.

    Can you make baked keto spaghetti squash ahead?

    You can easily make this recipe in advance by a day or two, and simply rewarm it in the oven to melt the cheese again.

    And the leftovers are absolutely delicious for a healthy breakfast with some eggs on top!

    More delicious keto spaghetti squash recipes

    • Cheeseburger Spaghetti Squash Casserole
    • Cheesy Slow Cooker Spaghetti Squash
    • Spaghetti Squash and Meatballs
    • Brown Butter Spaghetti Squash
    • Spaghetti Squash Egg Nests
    • Low Carb Chicken Spaghetti
    Titled image of twice baked spaghetti squash in the skin, in an oval dish. A fork is digging into it.

    Twice Baked Spaghetti Squash

    This keto spaghetti squash is twice baked for a delicious melty, cheesy side dish. It's easy to make and takes only 6 ingredients. And it's baked right in the shells for less mess and less clean up!
    5 from 11 votes
    Print Pin Rate
    Course: Side Dish
    Cuisine: American
    Keyword: keto spaghetti squash, oven baked spaghetti squash
    Prep Time: 15 minutes
    Cook Time: 1 hour 10 minutes
    Total Time: 1 hour 25 minutes
    Servings: 4 servings
    Calories: 186kcal

    Ingredients

    • 1 medium spaghetti squash (about 3 to 3.5 lb)
    • 2 tablespoon butter
    • 1 ounce Parmesan, grated
    • 2 cloves garlic, minced
    • 1 teaspoon dried crumbled basil
    • Salt and pepper to taste
    • 3 ounces sliced Provolone or mozzarella
    US Customary - Metric

    Instructions

    • Preheat the oven to 350F and line a large baking sheet with parchment paper.
    • Using a very sharp large knife, cut the squash in half lengthwise and scoop out and discard seeds. Place cut side down on the prepared baking sheet. Bake 60 to 75 minutes, until tender. You should be able to squeeze the outside of the squash and feel it give.
    • Remove and use a large spoon to scoop the flesh into a medium bowl, reserving the skins. Add the butter and let melt in the hot squash, then add the Parmesan, garlic, basil, salt and pepper. Toss until well combined
    • Divide the mixture between the reserved skins and top with sliced Provolone or mozzarella. Return to the oven and bake another 8 to 10 minutes, or until cheese is melted and bubbly.
    Nutrition Facts
    Twice Baked Spaghetti Squash
    Amount Per Serving (1 serving = ¾ cup)
    Calories 186 Calories from Fat 114
    % Daily Value*
    Fat 12.7g20%
    Carbohydrates 8.3g3%
    Fiber 1.7g7%
    Protein 8.9g18%
    * Percent Daily Values are based on a 2000 calorie diet.
    156.0K shares

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    Nutritional Disclaimer

    Please note that I am not a medical or nutritional professional. I am simply recounting and sharing my own experiences on this blog. Nothing I express here should be taken as medical advice and you should consult with your doctor before starting any diet or exercise program. I provide nutritional information for my recipes simply as a courtesy to my readers. It is calculated using MacGourmet software and I remove erythritol from the final carb count and net carb count, as it does not affect my own blood glucose levels. I do my best to be as accurate as possible but you should independently calculate nutritional information on your own before relying on them. I expressly disclaim any and all liability of any kind with respect to any act or omission wholly or in part in reliance on anything contained in this website.

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      Recipe Rating




    1. Betsy says

      May 13, 2021 at 10:23 am

      5 stars
      Super delicious! I love that this is Keto friendly! I love how easy this is, how delicious, and how it so wonderfully fits into my diet!

      Reply
    2. Bonnie says

      April 13, 2021 at 6:35 pm

      5 stars
      Saw this on Facebook and had to try it. Delicious!! And easy to make. I cooked the squash in the instant pot then followed the recipe and finished in the oven. I swapped cooper sharp cheese for the provolone. Hubby said it’s a keeper!! I agree.

      Reply
      • Carolyn says

        April 13, 2021 at 8:37 pm

        Glad to hear it!

        Reply
    3. Rumiko Adame says

      April 02, 2021 at 4:34 pm

      5 stars
      Sooooo good! We had this with your Air Fryer Steak Bites! My boyfriend says I can add this to the list of keto things he actually likes! 🙂

      Reply
      • Carolyn says

        April 02, 2021 at 7:03 pm

        Great combo! 🙂

        Reply
    4. 2pots2cook says

      March 18, 2021 at 5:25 am

      5 stars
      Extremely delicious meal ! Thank you for reminding me of this healthy and comforting dish since it is still so cold over here….

      Reply
      • Nancy Longenecker says

        March 19, 2021 at 8:23 pm

        This was wonderful but it makes so much. Can it be frozen?

        Reply
        • Carolyn says

          March 20, 2021 at 9:45 pm

          I honestly have not tried to freeze it…

          Reply
    5. Ethel Reedy says

      August 18, 2015 at 7:46 am

      Love the idea on baking it and freezing for winter. My garden is overflowing with squash. I hate seeing it go to waste. A lot of people have never eaten it.Great site love to read the comments

      Reply
    6. deb says

      August 03, 2015 at 4:48 pm

      This sounds heavenly!,I love ss but im onlyone in my family to eat it. Carbs are too high for my macros to have several days same week. Does it freeze well?

      Reply
      • Carolyn says

        August 03, 2015 at 6:01 pm

        I don’t think it would freeze but you could always just make a half recipe.

        Reply
    7. Val says

      July 21, 2015 at 10:19 am

      Hi! The produce person at Publix cuts mine in half for me, no extra charge!

      Reply
    8. Amanda says

      June 07, 2015 at 2:15 pm

      i bought my first spaghetti squash and just attempted to cut it and it was near impossible! My hands cramped up a bunch during the process and the fact that I didn’t lose a finger (or hand) during the process is pure luck. Do you have any tips for how to make it easier (and safer) to cut the spaghetti squash? Should I poke holes in it all over with a fork and microwave for a few minutes before I follow your recipe? It looks delicious but I have no idea how to cut the squash….

      Reply
      • Carolyn says

        June 07, 2015 at 4:15 pm

        Get yourself a very large and very sharp knife. And don’t get the ginormous squash, they are tougher and harder to cut. The smaller ones cook faster too. I don’t think microwaving it would do much to help.

        Reply
      • Susan says

        January 26, 2016 at 3:20 am

        Poke holes in the s.s. and microwave for about 5 minutes. Be careful when removing it from microwave as it will be hot. It will soften the skin making it easier to cut.

        Reply
    9. Tina K. says

      January 07, 2015 at 11:37 am

      I also cook mine in the microwave but a little different. I take an icepick and push it in deep on two sides so steam can escape as it cooks. Microwave on high 7-9 min. depending on the size. Take out with oven mitts as it’s very hot. Let it sit to cool down a bit then cut and scoop.
      Last summer I raised s.s. in my garden and was very successful. Every time I was 3 or 4 ahead I microwaved them, scraped the meat and froze them in serving size bags. Now I am enjoying it all winter when the price in the store is high. I decided to grow them when in the winter of 2013 I picked up one in the store and it was over $7!!

      Reply
    10. Pat says

      October 19, 2014 at 12:26 pm

      I cook spaghetti squash in the microwave too. Only I cook it whole. I wash it and use a fork and punch little holes all over it to let the steam escape. Cook on one side for 5 minutes, turn over and cook for another 5 minutes. It should feel soft when you take it out.
      It cuts its in half like butter (I have problem cutting them raw.) Be very careful taking them handling them after they are cooked. They are very hot.

      Reply
      • Carolyn says

        October 19, 2014 at 12:33 pm

        Sounds great, thanks!

        Reply
      • Carol B. says

        October 25, 2014 at 7:19 pm

        I tried this recipe tonight, and it was delicious. This is my first time cooking with spaghetti squash, in fact I’d never even heard of it. I was recently diagnosed with type 2 diabetes, and happened across this blog while searching for low carb recipes. I especially liked Pat’s microwave suggestion (thank you Pat). it really came in handy, as I had a hard time trying to cut the raw squash. Putting it in the microwave first worked great! Thank you Carolyn, for sharing. I will be adding this dish to my favorites!

        Reply
        • Carolyn says

          October 26, 2014 at 5:40 am

          Glad to hear it! So sorry for your diagnosis but please know that there are a million great ways to eat and control your diabetes.

          Reply
    11. Leslie says

      August 07, 2014 at 1:43 pm

      I cook spaghetti squash in the microwave. Cut in half and scoop out the seeds, put both halves on a plate face down and cook on high for 10-15mins (based on size – it should be very soft to the touch). Much faster, doesn’t heat up your house in the summer (we’re in Georgia) and a lot of water drains off onto the plate, so the squash isn’t as soupy when you add toppings.

      Reply
    12. carole says

      July 28, 2014 at 8:23 pm

      Could you please dump one of my replies? Don’t know how that happened; was trying to correct something, and both posted, sorry.

      Reply
      • Carolyn says

        July 29, 2014 at 5:23 am

        No worries!

        Reply
    13. carole says

      July 28, 2014 at 8:21 pm

      I first made spaghetti squash nearly twenty years ago. My mother in law fixed it a lot with butter, salt, etc, so when my husband and I started trying to lose weight and started running, I thought it would be a good substitute for pasta. I would use smoked sausage in my homemade spaghetti sauce, and scoop out the squash from the shell, and let the liquid drain away, and mix the sauce with the squash, and use parmesan cheese on top. We never missed the noodles, and it made eating healthier a lot easier. Now, my husband is a diabetic, and I am going back to some of the dishes that made getting healthy easier way back when, and it is working for him and us.

      Reply
    14. Penny Nelson says

      May 29, 2014 at 6:16 pm

      We have spaghetti squash at least once a week. We eat low carb, high fat diet to control diabetes. It works for us. Of course sugar is a no-no too..
      Thanks for new spin on for us an old favourite…
      Be Well

      Reply
      • Carolyn says

        May 29, 2014 at 6:20 pm

        I am with you on the LCHF for diabetes!

        Reply
    15. christine says

      April 30, 2014 at 12:27 pm

      Carolyn, I am on your sight daily so I thought today I would share with you some ideas I have come up with since my low carb journey seeing spaghetti squash is a staple in our household. I have gotten creative with the leftovers (after its been roasted in the oven) and taken a small onion or shallot and sauteed it with some olive oil then I mix in kale or spinach once it wilts I add to the spaghetti squash top with some Parmesan cheese and bake. This is a huge hit in our family and it had me thinking how I could make a mock baked ziti but replacing the pasta with the spaghetti squash. I made my sauce with spicy sausage (pork/chicken or turkey) the spicy sausage is key for flavor, I am not a fan so I actually do half sweet half hot. I then mixed it in with the already roasted spaghetti squash and topped with a mixture of ricotta (1/3 cup) parmesan (2 TBSP) and parsley (2 TBSP) put it back in the oven and let the cheese bake. I hope you enjoy!

      Reply
      • Carolyn says

        April 30, 2014 at 1:15 pm

        Thanks for sharing!

        Reply
    16. Michelle says

      April 30, 2014 at 12:13 pm

      Is there somewhere else the recipe is at? The page comes up blank in the content area (shows the menu and top logo/menu) in multiple web browsers for me.

      Reply
      • Carolyn says

        April 30, 2014 at 1:15 pm

        Something is up with their site so I let them know. Thanks!

        Reply
    17. Maggie Unzueta @ Mama Maggie's Kitchen says

      April 30, 2014 at 10:33 am

      I didn’t taste spaghetti squash until my early 30s. Craziness, I know! Now I’m hooked. Thanks for the recipe.

      Reply
    18. Barb says

      April 27, 2014 at 11:47 am

      Do you bake them cut side down?

      Reply
      • Carolyn says

        April 27, 2014 at 1:03 pm

        Yes, sorry. I should have specified that. Will amend!

        Reply
    19. sue/the view from great island says

      April 27, 2014 at 10:10 am

      I’m in love with this! I am probably the only one left on the planet who hasn’t tried spaghetti squash, and you’ve made it looks so incredibly tempting, I’m going on a hunt for it today. That top shot is wonderful, pinned!

      Reply
      • Carolyn says

        April 27, 2014 at 11:15 am

        Thanks, Sue! I can’t believe you haven’t tried it yet. It’s wonderful.

        Reply
    20. Sarah G says

      April 26, 2014 at 7:12 pm

      Oooh, brilliant usage of spaghetti squash! That’s going on the menu next week.

      Reply
      • Carolyn says

        April 27, 2014 at 6:30 am

        Thanks, Sarah!

        Reply
    Newer Comments »

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