Cheesy Baked Spaghetti Squash with Marinara Sauce
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This cheesy spaghetti squash casserole is vegetarian comfort food.
Spaghetti squash is a gift from the diet gods. When roasted, it miraculously transforms into low-carb, low-cal, spaghetti-like strands. Here, I toss it with good-quality jarred marinara sauce, top it with shredded cheese and crispy bread crumbs, and bake it until gooey and golden brown. The casserole makes a comforting vegetarian main course or side dish for meatballs or Italian sausage.
If you’ve never cooked spaghetti squash, it can be a little intimidating because it’s one of those large, awkward vegetables you’re not quite sure how to go at. For this recipe, I use two medium squash rather than one large one, as the smaller squash are easier to cut. I also sharpen my chef’s knife before I get started; it makes all the difference. (Pro tip: you’re much more likely to cut yourself with a dull knife than a sharp one. I use an electric knife sharpener regularly to keep my knives in tip-top shape.)
What You’ll Need To Make Cheesy Baked Spaghetti Squash
Step-by-Step Instructions
Step 1: Prep the Spaghetti Squash
Using a very sharp chef’s knife, cut a sliver off of the stem end of each squash (this creates a flat surface to cut the squash in half). 
Stand each squash upright on a cutting board and slice through them top to bottom to cut each squash in half (use your body weight to press the knife down).
Using a soup spoon, scrape out the seeds and discard them.
Step 2: Roast the Spaghetti Squash
Place the squash halves cut-side-up on a foil-lined baking sheet. Drizzle with the oil and sprinkle evenly with 1 teaspoon salt and 1/2 teaspoon pepper.
Flip the squash halves so they are cut-side-down.
Roast for 40 to 50 minutes, or until the squash is golden brown underneath and the flesh is tender when pierced with a fork. You should be able to scrape the strands away from the skin easily. Flip the squash halves so they are cut-side-up, and let sit until cool enough to handle.
Use a fork to scrape out and fluff the strands.
Step 3: Toss the Spaghetti Squash with Sauce and Seasonings
Increase the oven temperature to 425°F. Place the strands in a large bowl. Add the marinara sauce, 3/4 teaspoon salt, 1/4 teaspoon pepper, and thyme.
Toss gently until the squash is evenly coated. Taste and add adjust seasoning if necessary.
Step 4: Assemble and Bake
Transfer the mixture to a 9 x 13-inch baking dish.
Sprinkle the mozzarella cheese evenly over top, followed by the Parmigiano-Reggiano.
In a small bowl, combine the melted butter with the panko, and mix until the panko is evenly coated.
Sprinkle the panko mixture evenly over the cheese.
Bake for 25 to 30 minutes, or until the top is golden.
Let cool for a few minutes, then sprinkle with more fresh thyme and serve.
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Cheesy Baked Spaghetti Squash with Marinara Sauce
This cheesy spaghetti squash casserole is vegetarian comfort food.
Ingredients
- 2 medium spaghetti squash (about 2½ pounds each)
- 1 tablespoon extra-virgin olive oil
- Salt
- Freshly ground black pepper
- 1¾ cups jarred marinara sauce, best quality such as Rao's or Victoria
- 2 teaspoons chopped fresh thyme, plus more for serving (or ¾ teaspoon dried)
- 1½ cups shredded whole milk mozzarella cheese
- 3 tablespoons finely grated Parmigiano-Reggiano
- 1½ tablespoons unsalted butter, melted
- ¾ cup panko bread crumbs
Instructions
- Preheat the oven to 400°F and set an oven rack in the middle position. Line a baking sheet with heavy-duty aluminum foil for easy clean-up.
- Using a very sharp chef's knife, cut a sliver off of the stem end of each squash (this creates a flat surface to cut the squash in half). Stand each squash upright on a cutting board and slice through them top to bottom to cut each squash in half (use your body weight to press the knife down).
- Using a soup spoon, scrape out the seeds and discard them.
- Place the squash halves cut-side-up on the prepared baking sheet. Drizzle with the oil and sprinkle evenly with 1 teaspoon salt and ½ teaspoon pepper. Flip the squash halves so they are cut-side-down. Roast for 40 to 50 minutes, or until the squash is golden brown underneath and tender when pierced with a fork. You should be able to scrape the strands away from the skin easily. Flip the squash halves so they are cut-side-up, and let sit until cool enough to handle. Use a fork to scrape out and fluff the strands.
- Increase the oven temperature to 425°F.
- Place the strands in a large bowl. Add the marinara sauce, ¾ teaspoon salt, ¼ teaspoon pepper, and thyme and toss gently until the squash is evenly coated. Taste and add adjust seasoning if necessary. Transfer the mixture to an ungreased 9 x 13-inch baking dish. Sprinkle the mozzarella cheese evenly over top, followed by the Parmigiano-Reggiano.
- In a small bowl, combine the melted butter with the panko, and mix until the panko is evenly coated. Sprinkle the panko mixture evenly over the cheese. Bake for 25 to 30 minutes, or until the top is golden. Let cool for a few minutes, then sprinkle with more fresh thyme and serve.
- Make-Ahead/Freezer-Friendly Instructions: The casserole can be assembled and refrigerated for up to 2 days before baking, or frozen for up to 3 months. Bake directly from the refrigerator or freezer, allowing a few extra minutes in the oven.
Pair with
Nutrition Information
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- Per serving (6 servings)
- Calories: 452
- Fat: 26 g
- Saturated fat: 14 g
- Carbohydrates: 39 g
- Sugar: 16 g
- Fiber: 7 g
- Protein: 20 g
- Sodium: 1,252 mg
- Cholesterol: 70 mg
This website is written and produced for informational purposes only. I am not a certified nutritionist and the nutritional data on this site has not been evaluated or approved by a nutritionist or the Food and Drug Administration. Nutritional information is offered as a courtesy and should not be construed as a guarantee. The data is calculated through an online nutritional calculator, Edamam.com. Although I do my best to provide accurate nutritional information, these figures should be considered estimates only. Varying factors such as product types or brands purchased, natural fluctuations in fresh produce, and the way ingredients are processed change the effective nutritional information in any given recipe. Furthermore, different online calculators provide different results depending on their own nutrition fact sources and algorithms. To obtain the most accurate nutritional information in a given recipe, you should calculate the nutritional information with the actual ingredients used in your recipe, using your preferred nutrition calculator.
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Delicious!! Recipe is a keeper. Froze leftovers and they were tasty also.
This is terrific!! I had jalapeño jack cheese on hand and used that rather than mozzarella. Added a nice little kick. This will definitely be a go-to weekday dinner.
“World class” was my husband’s comment and I certainly agree! I had almost given up on spaghetti squash as it normally is very bland. Not this dish! You should have heard two carnivores roaring over this vegetarian delight.
Hi Jen, I love all your recipes and I credit you for making me a much better cook. I’m so glad you said to get two smaller size squash, It took all my strength to cut them. Because of you I’m getting a little more adventurous and last night I added leftover rotisserie chicken and sautéed some bell peppers and made this our main dish. My husband usually doesn’t like squash and he loved this dish. Thank you again.
This is fantastic. Mixing the marinara sauce with the spaghetti squash is brilliant- low fat. All of the “decadence” is on the top and shines. Thank you so much for all of your fantastic recipes and generosity. I know anything I make from your books or website is going to be delicious.
❤️
Unbelievably delicious as are all of Jenn’s recipes. My husband ate half of the 9 x 13 pan himself in one sitting. Points I would like to add and not sure if this was mentioned by another reviewer is to drain the strands once they are cooled and out of the shell. Had I not done that, it would have been too watery. In addition to the two 2.5 lbs of squash, I also added another small one to ensure there was plenty of squash to balance with all those (not so healthy) toppings. Super yummy.
I tried this and it was a hit. We served it with with Italian meatballs, but this would be a great side dish for fish or shrimp. There are only two of us but the leftovers were even better the next day. I will be making this the next time we have dinner guests as it can be made ahead. Bonus….The flavour is better the next day.
Really delicious dish. I had it for my main course and my husband and daughter ate it with Italian sausage and salad. I used vegan Parmesan to make it vegetarian. I wasn’t sure that they would like it, but both of them had seconds! If you roast the squash ahead of time, it all comes together in no time. Thanks for a great recipe!
Lonely spaghetti squash on my counter, and in comes this recipe. Oh my goodness! Absolutely delicious (and I am very much not a spaghetti squash fan!). I used Rao’s marinara. Don’t skimp on the thyme, it makes the dish. I already have plans to use this over Thanksgiving week with guests.
Hi Jen – I’ve been making your Spaghetti Squash Au Gratin recipe for years now & love it! I noticed you’ve replaced it with this recipe, which is similar yet slightly different (e.g., baking the squash as opposed to boiling). I’m sure it’s delicious (as all your recipes are). Out of curiosity, why did you make the change? Does it change the taste/nutritional value in some way?
Hi Lily, Sometimes the boiling method leaves the squash a bit watery, so these days I tend to roast it (I originally posted the recipe in 2009!). The flavor is a little more concentrated with the roasting method, as the sauce doesn’t get diluted, but it’s not a huge difference. Hope that helps! 🙂
Cannot wait to make this!
If I add the Italian sausage , is it best to pre cook the sausage and then add it to the marinara mixture?
Thanks so much
Hi Melissa, Yes that’s what I would do. Enjoy and please LMK how it turns out!
So I just want to say that I am a fan of Jenn’s recipes, use several on a regular basis and even own a couple of her cookbooks. I saw this recipe come through in my email today and just happened to have a spaghetti squash on the counter that I needed to use. I used Victoria’s marinara and followed the recipe exactly except for adding some browned Italian sausage to the
mixture. All my kiddos (aged 8 and younger) said it was AMAZING! Anytime an 8-yr old says a squash recipe is amazing, it’s a keeper! I will never make spaghetti squash any other way now.
This is delicious! I added spicy Italian sausage and omitted the bread crumbs (I didn’t have any on hand) Even my daughter who does not like spaghetti squash gave it a thumbs up.
Delicious! It was an EASY weeknight meal that even my 10 mo. old enjoyed. He’s used both hands to shovel it into his mouth. Minimal dishes was the cherry on top! Thanks for sharing this recipe 🙂
This recipe is delish…I am always Team Rao’s Marinara. In case you don’t have mozzarella on hand, I subbed a blend of Havarti and Swiss and it was wonderful! Thanks for all the great recipes Jenn!
I make this also—usually I keep some browned beef/sausage in the freezer if we want it with meat. I cook the spaghetti squash in the IP—no piercing required—for about 9 minutes.
I enjoy your recipes!
Fantastic, everyone loved it! I think this recipe has special touches to make it better than most people think of when they think of spaghetti squash. I used the Rao sauce and it was perfect; carmelized nicely. I cooked my squash the day before, and let it drain overnight which eliminated a lot of liquid for the particular squash I had. I think it would have had too much liquid otherwise. Used homemade breadcrumbs, double the amount; and it gave it a nice crunch. Thank you for this family-pleaser.
Great recipe for summer vegetables. This squash au gratin was a great start to a dish. I added a whole diced tomato, couple of peppers and some Italian meatballs to this dish. I needed to use up my fresh vegetables from the garden. I do feel that I could add more herbs and spices to give it a little bit more flavor. But it was excellent and I would make it again in a heartbeat.
Awesome dish to satisfy pasta craving without the carbs. Easy to make other than waiting for the squash to cook. 🙂
Would this work with any Squash ? I am in Europe and having a very hard time find finding Spaghetti Squash as the season has just ended here.
Unfortunately not 🙁
This recipe looks delicious. I’m curious as to why the sodium count is so high, is it primarily from the marinara sauce?
Hi Gretchen, the majority of the sodium would come from the combination of the added salt, marinara sauce, and the cheese. Feel free to cut back on the added salt and add more to taste when serving. Hope that helps!
My husband and I like this recipe! Would it work to make it up until the baking point, and then put in the refrigerator, and then bake later? What would you suggest to prep this for dinner ahead of time? (In the morning or day before)
Hi Heather, I definitely think you could assemble this ahead and refrigerate. If given the choice, I’d probably do it the morning before (and glad you like it)!
Absolutely delicious! You cannot overcook. Let it get nice and browned. YUMMMMM
Easy to make and absolutely delicious. Loved it.
Jenn, your spaghetti squash recipe was AWESOME! I followed the recipe exactly (even using Rao’s marina sauce which I could have eaten out of the jar) …no substitutes! It was a BIG hit with my family …my son-in-law went back for seconds, or was it thirds?
How will this hold up if I assemble it one day and bake & eat it the next? Or will it be better if I assemble & bake one day and reheat the next? Thank You.
Hi Kate, I think you could go either way with good results. Hope you enjoy!
I do not like to buy marinara sauces, too much salt and sugar. Any suggestion for best home made version that would have right texture for these recipes?
Hi Susan, This one would work well.
Spaghetti squash is difficult to find here in Portugal, could ordinary butternut squash be used instead in this recipe?
Unfortunately, because butternut squash doesn’t form spaghetti-like strands, it won’t work here– sorry!
Does this freeze well?
Hi Karen, I’ve never frozen this so I can’t say for sure, but I suspect you could freeze it.
My roommate and I just discovered the joy of squash and have enjoyed the leftovers of this recipe everyday for fantastic lunches!
This was my first experience with spaghetti squash. I’ve been skeptical, but how exciting that it really does work as a delicious pasta substitute! I made this with my homemade tomato sauce with sausage, au gratin per Jen’s recipe. The following week, I used the other half of the squash (which I had frozen) with a white clam-and-shrimp sauce. Also incredible! I think next time I’ll try without cutting the squash in half so that I can get nice, long “noodle” strands. Fabulous.
OMG!!!! Have tried to make spaghetti squash 2-3 times over the years and have been more than a little disappointed. No more! I just made this recipe, using ingredients I had on had (i.e., no panko bread crumbs, just plain; mozzarella and cheddar, no Italian cheese blend; and I had a meat sauce in the freezer).
Can I say I’m moaning with delight in every bite!!!! Cannot wait to take leftovers to work and share the love. This recipe is a hit.
Wow wow wow! This was delicious! Very filling and so easy to assemble. Can’t wait to make this one again.
Delicious and easy. I was very pleased with myself for serving this dish up. Reheated well for leftovers too.
Thanks for sharing the “reheated well for leftovers”! I live alone, and hesitate to make some dishes, because I eat leftovers ALL THE TIME! So glad to know in advance!
How do you keep the spaghetti squash from getting soggy? I usually roast it or microwave it and when I scoop it out, there’s always so much water in the bowl. Do you drain it repeatedly?
You can certainly drain it or, if you want to get even more water out, you can squeeze it gently with a clean dish towel.
Love this recipe. Even my picky eater ate this!
Hi Jenn,
Would you serve this with your glazed chicken meatballs?
Absolutely!
Hey Jennifer! I’ve never made spaghetti squash before but am going to try this recipe! It looks awesome! How well will the squash stand up as leftovers? I’ll be cooking this only for myself so will have 3 portions leftover that I’ll probably use to bring as lunches to work. Will the squash keep its spaghetti shape or will it get mushy? Just curious…thanks!
It holds up beautifully so no worries….you can reheat in oven or microwave. Hope you enjoy it!
Oh good, thank you!
Jenn, I made this tonight and it was AWESOME! Instead of using jarred sauce I used homemade turkey bolognese (I wanted some more protein in it). It was my first time cooking with spaghetti squash and it definitely won’t be my last. Thank you for a delicious recipe!
I might have to try this for my kids and see if they notice it isn’t real spaghetti. Great way to limit calories and carbs for me too!
My oldest son always begs me to buy spaghetti squash and I never do because I don’t like it. Next time he asks, I will buy some and try this recipe. This recipe will make us all happy I think.
I have a trick for you…..puncture the spaghetti squash with a knife all over and microwave each one for ten minutes. So much easier than trying to cut them raw…and faster than boiling!
Never knew how to make a dish with Spaghetti Squash. This was wonderful,Jenn.Ironically, made it the next night right after Heather did. Shared it with all my teacher friends and they loved it also. I sent them your site Thanks!
I have made this twice already, and last night when I served it my husband exclaimed, “Yay! You made my favorite dish!” My husband cannot eat gluten, and this tastes much better than any rice pasta we have made. I love it also and did not feel guilty indulging in seconds. Instead of the panko, I used Aleia’s brand seasoned GF breadcrumbs – still tasted delicious without the gluten! I prepped the squash earlier in the day – you can boil it and scoop out the spaghetti strands and put them in the refrigerator until you are ready to combine them with the other ingredients and bake. Saves time and effort at dinnertime!
Hi Heather! Have you tried Jovial GF pasta? It’s my favorite! ~Julie
I second the Jovial recommendation. My current favorite is Ronzoni. I’ve even used it in recipes for non-gluten-free friends, and they can hardly tell the difference.
Jenn, you are a genius! This dish was amazing and even my kids ate it.
This recipe was incredible!!! I have never cooked spaghetti squash before and this method was full proof. I truly felt like I was eating spaghetti and knowing I could eat more and more without the guilt, was amazing!!! Thanks for this recipe, you made my day!!!
Made this for dinner last night and my whole family loved it. I never made spaghetti squash before but always wanted to try. Thanks!
This was yummy.
I used freshly grated fontina, asiago and some Parm for the cheese topping, and the panko bread crumbs gave it a nice crunch.
When I made this (years ago) I baked it, and it came out mushy. With your boiling method, the strands were perfectly separated and held their shape. Love it.
I served it with meatballs so my meat loving hubby would not be asking “Where’s the beef?” LOL (he loved it btw)
Love squash – love cheese/cream — can wait to try this one
http://mydinnerswithrichard.blogspot.com/
Looks amazing!
I recently made this using a lite alfredo sauce, mushrooms and grilled chicken. My husband thought I was a culinary god – he was totally mesmerized.
I’m glad to get your reminder about spaghetti squash. It’s a great dish that somehow got dropped from my already sparse repertoire. And the instruction for cutting it will prevent the awful mess I made the first time I made it.
Thanks.
I’ve been obsessed w spaghetti squash lately. That looks great, will have to try it asap. =)