Twice-Baked Spaghetti Squash and Cheese
All the comfort of traditional mac and cheese, but with veggies! This twice-baked spaghetti squash and cheese is sure to become one of your favorites.
While my love for pasta is strong and unwavering, I have wholeheartedly jumped on the spaghetti-squash-in-place-of-actual-pasta bandwagon. Sometimes you just have to swap out the carbs for some veggies.
So every so often I “healthify” one of our regular pasta dishes with spaghetti squash, and I have yet to hear complaints from my family. I first posted this twice baked spaghetti squash and cheese recipe in 2015 and it’s been a favorite ever since!
It’s so creamy and cheesy, with great flavor from the roasted spaghetti squash and a nice crunch from the topping of toasted breadcrumbs.
What is Twice Baked Spaghetti Squash?
It’s just like it sounds! First, roast the spaghetti squash in the oven until tender (though you can also do this step in the microwave or instant pot, see below). Then, you shred the flesh with a fork and add whatever sauces or mix-ins to the squash you want— for this recipe I’m using a cheese sauce— and bake it until it’s hot and bubbly.
It’s so good! One of the favorite comfort foods.
Ingredients need to make this Twice Baked Spaghetti Squash and Cheese
Here’s what you’ll need:
- 2 medium-sized spaghetti squash
- Butter
- All-purpose flour
- Mustard powder
- Milk
- Sharp cheddar cheese
- Panko breadcrumbs
How to Cut Spaghetti Squash
We can all agree that cutting large squashes like butternut, acorn, and spaghetti squash isn’t always easy, right? This is the method that works for me:
- Place spaghetti squash on it’s side on a cutting board. Using a sharp knife, cut off the end with the stem so you have a flat edge.
- Place that flat edge flat on the cutting board so the squash is sticking up.
- Use a sharp knife (very important) to slice the squash in half from top to bottom. A serrated knife is helpful because it helps saw through the tough exterior of the squash, but a sharp chefs knife will work too.
This video makes it look so easy!
Once the spaghetti squash is halved, remove the seeds and pulp with a spoon and discard. Then, it’s for cooking.
How to Cook Spaghetti Squash
Roast in the oven— The most traditional way to cook spaghetti squash is to roast it in the oven. And honestly, I think the spaghetti squash tastes the best this way. Simply drizzle with olive oil and season with salt and pepper, then roast on a lined sheet pan at 375ºF until tender (about 45-60 minutes).
In the instant pot— This is definitely the quickest way to cook spaghetti squash! Though depending on the size of your squash, you may only be able to cook a few at a time. Place trivet inside your instant pot, then fill with 1 cup water and add the spaghetti squash. Set high pressure to 6 minutes and use a quick release.
In the microwave— The microwave is another great option too to cut down on time. Place spaghetti squash cut side-down into a microwave-safe dish that will fit your microwave and add 1/2 cup water. Microwave on high for about 15 minutes until fork tender (time will vary based on side of spaghetti squash).
The Creamiest Cheese Sauce
There’s nothing cozier than a homemade cheese sauce, and this is easily my favorite part of this dish! Roasted spaghetti squash is tasty on it’s own, but this cheese sauce takes it to a whole new level of flavor.
This is a simple cheese sauce that starts with a roux of butter and flour, then you add milk, cheese, mustard powder, and salt and pepper. It’s smooth, creamy, and oh so cheesy. A sprinkling of breadcrumbs is the final touch.
After another quick bake in the oven, this twice baked spaghetti squash is cheesy, cozy, and so satisfying. Serve it as a light meatless meal, or serve it as a side dish!
Other veggie-full recipe to love:
- Butternut Squash, Mushroom, and Poblano Enchiladas
- Coconut Rice Veggie Bowls
- Roasted Vegetable Asiago Fettuccine Alfredo
- Mushroom Ragu with Cheesy Polenta
Shop Tools for this Recipe
This recipe was originally published February 2015.
Twice Baked Spaghetti Squash and Cheese
Ingredients
- 2 medium spaghetti squash , halved lengthwise and seeds removed
- Olive oil , for drizzling
- 3 tablespoons butter , divided
- 2 tablespoons all-purpose flour
- 1 teaspoon mustard powder
- 2 cups milk (can use skim, 1%, 2% or whole)
- 8 ounces sharp cheddar cheese , shredded
- 1 teaspoon salt
- 1/4 teaspoon ground pepper
- 1 cup panko bread crumbs
Instructions
- Preheat oven to 375 degrees F. Line a sheet pan with parchment paper or foil.
- Drizzle squash with olive oil and season with salt and pepper. Place cut side-down on prepared sheet pan and bake until fork tender, about 45-60 minutes.
- Let spaghetti squash sit a few minutes until cool enough to handle, then shred flesh with a fork.
- In a large skillet, melt 2 tablespoons of the butter. Add flour and stir with a whisk until it makes a thick paste.
- Slowly pour the milk into the pan while whisking constantly. Bring to a boil, then cook for a few minutes until thickened, stirring frequently.
- Add the cheddar cheese, mustard powder, salt and pepper and stir until smooth.
- Add spaghetti squash and toss until combined. Divide evenly into the 4 squash skins.
- Melt the remaining 1 tablespoon of butter. Add the panko bread crumbs and stir until all the bread crumbs are moistened. Sprinkle on top of the spaghetti squash.
- Bake until filling is bubbling and topping is browned, about 20 minutes. Serve immediately.
- To cook spaghetti squash in instant pot: Place trivet inside your instant pot, then fill with 1 cup water and add the spaghetti squash. Set high pressure to 6 minutes and use a quick release.
- To cook spaghetti squash in the microwave: Place spaghetti squash cut side-down into a microwave-safe dish that will fit your microwave and add 1/2 cup water. Microwave on high for about 15 minutes until fork tender (time will vary based on side of spaghetti squash).
75 Comments on “Twice-Baked Spaghetti Squash and Cheese”
Total genius!! Baked spaghetti squash is good, but twice baked?! YES!
What is step number 4? Thanks.
This looks delicious! I have yet to try spaghetti squash in place of pasta but I’ve been wanting to for a while. This looks like the perfect recipe to start with!
This recipe definitely fits your site – it looks completely delicious! Love your cream cooking tip in the middle too!
Amazing! This is SUCH a beautiful recipe!!
Oh my gosh this looks heavenly.
I want oodles and oodles of this spaghetti squash!!
Oh yum. Just made this and it is amazing!!! Thank you.
Made this tonight. Added sautéed kale and garlic when mixing in the bowl. Turned out excellent! Loved it! Will definitely make this guilt free Mac and cheese again!
Love the idea of adding kale and garlic – yum!
Just made and it is delicious!!
I’m so glad! Thanks Lisa!
I made spaghetti squash for the first time last night and LOVED it! I started eating gluten free recently, and my gluten-eating BF was craving pasta I tried spaghetti squash. He tried a bit of mine, and liked it – so it looks like i’ll be searching out more spaghetti squash recipes!
Hello! Do you know the nutritional values for this recipe???
I don’t calculate any of that info, sorry!
I calculated it at 275 calories/ 18 carbs per cup. My recipe made 8 cups.
I have diabetes. I know this isn’t 100% carb-free. But what I really need is the protein content. It looks low. I may try this using my regular mac n cheese recipe instead of the roux. I’ll let you know how it turns out.
Looks delicious.
Thanks for the recipe.
Wish it had nutrition facts to check out….as I’m trying to stay on low card eating…..
Looks great but I need nutritional information.
You can also cook spaghetti squash in the microwave. Cut squash in half lenghthwise , remove the seeds. place in glass baking dish, pulp side down and add about an inch of water. Cook in microwave on high for twenty minutes. Some recipes say to put olive oil on the on the pulp side. I don’t and it always comes out great. Saves you 40 minutes of cooking time compared to baking in the the oven!
This one is a keeper!
How do I cook the squash? Cut side up or down. The video shows down but the instructions say cut side up. Is there really a difference? Thanks
The recipe says cool the onions 5 minutes until translucent. I think it should be cook not cool.
You Say its lower carb but there is no nutritional info. Without that info it could be 6000 carbs as opposed to 60000. Neither of which I want to consume.
It’s a LOWER carb meal simply because it’s using a veggie instead of pasta, but this dish is not “low carb”. I’m working on adding nutritional info to all of my recipes, but it’s not an easy task. In the meantime you are welcome to plug the recipe into any free online nutrition calculators!
Panko bread crumbs, onions, milk. Even without nutrition facts I know this won’t be “low carb” enough for my diet.
Yep, this is definitely not “low carb”. Maybe a little lower in carbs since there’s no pasta, but I have not labeled it “low carb”. Sorry this won’t work for you!
Made this recipe tonight and it was delicious! Can’t wait to bring it for lunch to work tomorrow. I didn’t have any panko breadcrumbs so I used seasoned Italian. I think the panko would be better so will make sure I have it next time I make this. Thanks for the recipe!
Hi Teri! Thanks so much for the comment, I’m happy to hear you enjoyed it!
What are the Weight Watchers SP on this please?? It looks delicious, spaghetti squash is new to me and I love it! Always looking for new ways to prepare it. Thanks..
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Hi Velma! I don’t calculate WW points for my recipes, but you’re welcome to plug the ingredients into their calculator and do it yourself. 🙂
Wow! I calculated it out and if I divide it into 4 servings and use 1% milk, it works out to roughly 20 Points a serving! I think NOT!
I’m not surprised. This isn’t meant to be a low-cal recipe, but a slightly healthier, fun, veggie-filled alternative to traditional baked mac and cheese. I bet it’s waaayy more points with pasta. Maybe an option next time you just have to have mac and cheese? Or not, I’m sure there are plenty of more WW-friendly mac and cheese recipes out there. 🙂
Best recipe yet. It came out perfect and definitely not mushy! It’s pinned and saved for next time!
Yay! So happy you loved the recipe.
This is a family favorite! Its soo yummy! No need to worry about ” not low calorie/carb” if you dont like it choose healthier substitutes or just dont make it! 🙂 I used almond flour and skim milk and cornflakes instead of bread crumbs. I highly recommend this recipe! It will be 2 meals for myself and my husband. I added up to be 332 calories for of 1 half of squash. Thanks so much for the recipe!!!
Wonderful! Thanks so much for the feedback, Michelle!
Can you substitute the milk for almond for a lactose intolerant person. Im fine with cheese just not cows milk. Everything else is good. Looks so good
Yes I think that should work fine!
Love spaghetti squash anyway. Always looking for new ways to prepare them. I’m not fond of cheddar, so I substituted cold-jack cheese. Mmm, mild but still cheesy.
Wonderful! Thanks so much
Total genius!! Baked spaghetti squash is good, but twice baked?! YES!
Delicious!…My oven is going to be pretty full this Christmas Eve. I want to make this for Christmas Eve dinner and was wondering if twice baked spaghetti squash.
I just made this and was curious about the calories as well. Putting the ingredients into a calculator, it comes to 560 calories for 4 servings. Which isn’t that bad. It’s def not low calorie. The 5 tablespoons of butter don’t help lol. But I added broccoli and it’s a nicely indulgent meal. Thanks!
Yes, this is not a low calorie meal. 🙂 But it’s lower than if you used pasta and I like the extra dose of veggies.
Really so delicious! I love it
I like most recipes that are offered on certain food blogs but I’m not sure about this one. Me and Squash don’t mix.
Thank you for sharing recipe about Spaghetti Squash
Hi Annalise, Your food looks so cheesy and tempting. I love baking too. I also find new recipes and try myself at home. And now I think, I am inspired by you and gonna try this cheesy recipe at home. Thanks for sharing. you should definitely make your own show on any channel or on youtube.
This has quickly become one of our all time favorites! My husband asks for it all the time!
Hey Annalise,
As I said earlier, that I am going to try this recipe and I did. My friends started asking me about it. And they also want this delicious spaghetti squash cheese. Thank you very much.
I love to eat baked goods, but I’ve never eaten this dish, maybe I’ll try it in the future
As tasty as caloric. Somebody stop me to eat it!
very delicious and tsaty in will try this
I love very much baked spaghetti. I will definitely try it.
The best recipe for my family. It came out perfect and definitely not mushy! It’s pinned and saved for next time!
Beautiful ideas I can’t wait to try this recipe, Thank you for share! i like this
very nytc
I love very much baked spaghetti. I will definitely try it. Thanks for sharing this article.
wowww its so yummy!! thanks for sharing such delicious recipe. i m really exciting to make it.
As tasty as caloric. Somebody stop me to eat it.
Really so delicious! I love it
Amazing! This is SUCH a beautiful recipe!
Oh my gosh this looks heavenly.
Oh yum. Just made this and it is amazing!!!
Love the idea of adding kale and garlic – yum!!
Really so delicious! I love it Going to share this with my beautiful wife!
Thank you very much. I look forward to your next share
very interesting article. I really enjoyed it. Thanks
Wonderful! Thanks For Sharing
Wonderful! Thanks For Sharing
This looks delicious, and I appreciate all your helpful notes and tips! Bookmarking for this weekend 🙂
Harold Burton
Love this recipe! I have made it a couple of times before and will be making it again tonight but adding some shrimp and maybe some spinach!
Love this roundup idea! I am making a “basics” cookbook for a few of my girlfriends who are getting married this summer. Definitely going to include some of these ideas!