Baked Spaghetti Squash and Cheese
This easy, cheesy baked spaghetti squash is a healthier take on mac and cheese! It’s cheesy, loaded with vegetables and feels like comfort food, without the calories and carbs.

Baked Spaghetti Squash and Cheese
I was craving something cheesy, without all the carbs from macaroni and came up with this dish back in 2003. I basically swapped the pasta from my Macaroni and Cheese recipe with roasted spaghetti squash and the results were this wonderful! The squash takes on a fantastic texture when baked in the cheese sauce.
This can easily be prepared ahead, then baked just before ready to serve. I reheated leftovers in the microwave for lunch the next day and it was just as good as when I first made it. Great as a main dish or a side.
How To Make Baked Spaghetti Squash
If you’re new to making this winter squash, you don’t have to peel it. Cut the squash in half lengthwise or down the middle for longer strands, scoop out the seeds and bake.
Once the spaghetti squash is baked and removed from the shell, there will be a lot of liquid. I recommend wringing it with paper towels or a cheesecloth to avoid this from being too soggy.
Spaghetti Squash and Cheese Variations:
- You can try making this with different cheese combos. Try a mix of cheddar and Swiss, or swap it for Havari.
- Add some breadcrumbs to the Parmesan topping at the end for some texture.
- Add some cooked chicken sausage for added protein.
- Make a tuna spaghetti squash casserole buy swapping spinach for tuna and peas
More spaghetti squash recipes you might enjoy:
- Spaghetti Squash Enchilada Bowls
- Spaghetti Squash with Bacon and Parmesan
- Spaghetti Squash Primavera
- Spaghetti Squash Lasagna
- Roasted Spaghetti Squash

Baked Spaghetti Squash and Cheese
Cheesy baked spaghetti squash and baby spinach – a comforting, cheesy dish, without the guilt. Perfect for Meatless Mondays or any day of the week!
Ingredients:
- 5 1/2 cups cooked spaghetti squash (from about 2 small) see directions below:
- 1 tbsp butter
- 1 tbsp olive oil
- 1/4 cup minced onion
- 1/4 cup flour (use ap gluten-free flour for GF)
- 2 cups skim milk
- 1 cup fat free chicken broth (vegetable broth for vegetarian)
- 2 cups (8 oz) Sargento 2% reduced fat mild cheddar
- salt and pepper, to taste
- 4 cups (about 4 oz) baby spinach
- 1/8 cup grated parmesan
Directions:
- Preheat the oven to 375ºF.
- Cut the squash in half lengthwise; remove and discard seeds. Place squash on a baking sheet cut side down. Bake until tender, about 1 hour.
- Separate the strands of squash with a fork and place in a medium bowl; discard shells. Squeeze out any excess liquid from the squash if watery.
- Maintain the oven temperature.
- Heat butter and oil in a large saucepan over medium heat. Add onions and cook about 2 minutes.
- Stir in flour. Reduce heat to low and cook, stirring continually 3 – 4 minutes.
- Add milk and chicken broth and continue whisking, raising heat to medium-high until it comes to a boil and becomes smooth and thick, about 2 minutes stirring; season with salt and pepper.
- Once it becomes thick, remove from heat, add cheddar cheese and mix well until cheese is melted.
- Adjust salt and pepper to taste, add cooked spaghetti squash and baby spinach, pour into a baking dish and sprinkle parmesan cheese on top.
- Bake until bubbly and golden 25 to 30 minutes.
Nutrition Information
Yield: 7 servings, Serving Size: 1 cup
- Amount Per Serving:
- Freestyle Points: 6
- Points +: 5
- Calories: 165 calories
- Total Fat: 8g
- Saturated Fat: 2g
- Cholesterol: 7.5mg
- Sodium: 278.5mg
- Carbohydrates: 16g
- Fiber: 2g
- Sugar: 6.5g
- Protein: 10g
So good! I made the spaghetti squash the night before and squeezed out as much of the moisture as I could before storing it between 2 paper towels in a container. I noticed a lot of people commented that it came out soupy. I did it like this and had no issues when I prepared the dish the next day.
Did you use 1 squash or 2?
I usually use two smaller squashes, but sometimes I am able to find a large one.
Could you use butternut squash instead?
I wouldn’t think so, the texture of butternut is much different than spaghetti squash. When I cook butternut for pies, it just gets soft.
Is the spinach to be cooked first?
No I wouldnt, the spinach should cook when you bake the dish for the last time.
I made this and used almond milk and kale instead of spinach and it came out great. Thanks for a great recipe.
What is the serving size for 6 points
The recipe says a serving is 1 cup.
What is the serving size
I made this for the first time tonight (the vegetarian version, with vegetable broth) and it came out delicious! The only modifications I made were using full-fat milk (reduced to 1.5 cups based on other reviews) and full-fat cheese (our house doesn’t do low fat;-). Based on other reviews and my own previous experience, I did a very thorough job squeezing the water out of the squash after turning it into spaghetti strands. The dish was not watery AT ALL and there was the perfect amount of sauce that clung nicely to the squash noodles. My husband enjoyed it even though he is not a squash person. The only change I plan to make next time is adding mushrooms as another reviewer suggested as this dish could use a little more variety of texture. Overall, very pleased with this yummy and healthy dish that tastes like pure comfort food. 🙂
Do you think this can be done in the pressure cooker?
Diana, I have cooked the squash in the IP before and it came out great! It was very quick but I’m sorry I can’t recall now how many minutes it was now. I’m sure you can find out though easily enough. I don’t know about making the entire recipe in the IP though if thats what you meant.
7 minutes at high pressure and then quick release. I did it last night and it came out great!
The recipe says a serving is 1 cup.
Looks delicious.
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Epic, soooooooooo good!! Microwaved the spaghetti squash and gave it a quick squeeze in paper towels. Otherwose, made it per the recipe, loved it!! This is a keeper
Super delicious and weirdly filling! I used Tillamook cheddar, 1.25 cups of 2% milk, and a little extra onion and it came out perfect. It has so few calories even with my changes that I was ready to have two servings, but I was stuffed after one. I did let the sauce thicken a little longer than suggested, and I squeezed out the spaghetti squash with cheesecloth. Even then I think I would use 1 cup of milk and .75 of broth next time. Awesome recipe!
This was so delicious my husband and I couldn’t stop eating it! The first time I made it exactly to the recipe and the second time I added some turkey sausage crumbles to serve as a main dish. This recipe is a keeper!
I would give this 10 stars if possible. Made the recipe to the letter and squeezed out all the excess squash liquid with a dish cloth. It came out perfect and tasted thrillingly decadent. Gina, every single recipe of yours that I’ve made has been fantastic. You’ve actually made dieting fun for me!
I’m glad Lisa!
Do you think it would be okay to use unsweetened almond milk as a substitute for skim milk ?
thanks
Yes!
I always use unsweetened almond milk!
This is delicious!!! I’ve made several variations of this dish, keeping the cheese sauce the same, and always using spaghetti squash, but I add whatever veggies I have on hand. I have also added chicken sausage and made it a main dish.
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Made this tonight but think I did something wrong. The taste was excellent but I think I squeezed the squash too much. It was stringy before but after squeezing it was a lot less volume and clumped together. I guess i was afraid of leaving it too wet. Mixed it together as well as I could and decided to go for it anyways. Taste was still great will have try again.
Will this freeze ok?
I dont think so
I made this for the first time for dinner tonight. My family was in awe of the full flavor while the calorie count being so low. It is definitely going to be added to my rotation of monthly meals. <3
This was fantastic – and way better leftover but isn’t that always the case with casseroles? I got 2 of what I’d call medium spaghetti squashes and they made the exact amount needed for this recipe. I added about 1/3 pound of cooked bacon and a whole 5oz package of baby spinach and for cheese I used the Mac & Cheese shredded blend from my local grocer (Cheddar, American & Swiss). I also used whole milk and full fat cheese to suit our diet and tastes.
This was boyfriend approved as well (not that he’s super picky) and we may be sharing this with our band-mates soon.
Keep up the great work Gina! Big fan!
Why do I always have trouble trying to print your recipes? You give us the print recipe option. I have an HP printer. Never works when I use print recipe option. I even take it over to chrome and try. What am I doing wrong? Love your recipes!
Robin Renner
Made this as part of a Thanksgiving meal. While the spaghetti squash and cheese is good, it lacked something. I added garlic to my dish but think next time I make I will add a few more spices to really give it a kick. Thinking of using the cheese base as a way to make a low fat version of hashbrown casserole.
This was amazing!!! It was so hard to eat only 1 cup. Do you think it would freeze well? I have so much left. How long will it last in the fridge (assuming about a week)?
I keep trying to like spaghetti squash and I just don’t, but being the mac and cheese lover that I am, and being on weight watcher’s, you’ve given me a reason to give it another try.
I only have 1 spaghetti squash, didn’t see I needed 2 would that be enough? Can I add pasta to it maybe?
Depends on how many cups of cooked spaghetti squash comes out of it, may have to halve the recipe.
This recipe is the bomb! I did the tuna noodle casserole. Oh so yummy. I also did it all paleo compliant! Brilliant! ♥♥♥
So yummy, and I can see the cheese sauce being used for other dishes. Thanks!
Holy CRAP I need to try this!!! We’ve been doing boring spaghetti squash and store-bought marinara + ground beef for a while but this just cranked it up to 11.
I am down 30lbs thanks to SkinnyTaste but sometimes miss my comfort foods. This feels like cheating but I’m okay with it. 🙂
Amazing!
If I were to make this ahead then bake when needed, where is the stopping point? Also, any recommendations on baking time changes if I were to bake later after refrigeration? TIA!
PS, everything I’ve ever made from your blog has been absolutely amazing!
How much saturated fat is there? It doesn’t give one. I made this tonight and it was super yummy! Will definitely squeeze out moisture next time as it was a bit runny but it’s going to be a new staple in my house for sure.
Glad you enjoyed! The saturated fat is 2g.
Easy tip. I pierced skin with knife around half cutting line. Put in microwave 10/15 minutes ( depending on size) let cool. It cut very easy, discarded seeds and scraped out.I added cut up broccoli instead of spinach. Was a great side dish. Would also make a good vegetarian main dish.
I am making this now and realize I only have rice flour or almond flour. Will one of these work?
Commented the other day when I made this dish. I had leftovers. Today, I added chicken broth and more broccoli and made a delicious soup.
Delicious!! Hit the healthy cheesy food craving we had been having. Will definitely make and will make again soon!
Super creamy. Added garlic and mustard powder for flavor and I had only 1 small squash so needed filller… added a bag of mixed veggies. Turned out great!
I made this for lunch and it is really so good. I normally don’t care much for spaghetti squash, but this cheese sauce is wonderful. I didn’t wring out any water from my baked squash, but I did use 1/2 cup less milk than the original recipe cited and the final dish was perfect.
Squeezing the water from the squash sort of ruined it. The onions were OK, but they don’t really go in mac n cheese and I don’t see how they went well with this version either. The baby spinach was a nice touch to the sauce.
Any chance this is decent with beef broth?
This is a new favorite. I could eat the entire pan. I may make this as a side for Thanksgiving but it’s a great main dish as well. I added some cooked baby bells and it was filling!
This sounds amazing! Can’t wait to try it! I’d like to try this for my son & daughter-in-law (they’re vegetarians) but my daughter-in-law is also dairy free (for medical reasons). I’m very new to the dairy free cooking and I am looking for any tried and true substitutions for cheese. I’ll use plain almond milk for the skim milk but have no idea for the cheese. Any ideas?
I made this last night, even my 2 1/2 year old grandson ate it! (although I had to tell him it was spaghetti with butter on it) He had a huge bowl of it. So good, and leftovers! 🙂 Thank you Gina, have a lot of spaghetti squash so going to check out your other recipes.
ABSOLUTELY delicious! I found another recipe with spaghetti squash that I can use. It’s full of flavor. I can feel good about eating a good bit since it’s less carbs. Thanks for sharing this wonderful recipe!
Sounds great. Could you substitute Almond flour or. Coconut flour
Do I need to use 2 squash or will 1 do?
This recipe took a bit of time to make the sauce, BUT…OMG!!! It was wonderful. This has nothing to do with me preparing it, but it tasted like something I would order at a fancy restaurant. I had 1 large squash, so I only microwaved half for this dish. I was about 3/4 cup short on the 5-1/2 cups for the complete recipe. However, I knowingly made the full batch of sauce, so I would have that “cheesy love” I had been craving.I will definitely make this again, and very would love to serve this at a dinner party!Thank you for my Friday delight!
I love this recipe! It totally satisfied my mac & cheese craving. I can’t wait to make it again! Definitely make sure to get as much liquid out of the squash as possible.
Just made this and it came out so amazingly. A healthier option that is so filling, so tasty, and perfect for these cold winter months. I also threw in some broccoli with the spinach, and would maybe add cauliflower or peppers next time, even chicken if I wanted a little more protein! Thanks so much!