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Baked Spaghetti Squash and Cheese Recipe

Published: Sep 22, 2026 by Ivy · This post may contain affiliate links · Leave a Comment

Jump to Recipe·4 from 47 reviews

If you’ve never tried a Baked Spaghetti Squash and Cheese Recipe, you are in for an incredible treat that feels like a warm hug on a plate. This dish transforms humble spaghetti squash into a creamy, cheesy, and comforting casserole that’s perfect for cozy dinners or sharing with friends. With gooey cheddar, tender strands of squash, and a lovely hint of parmesan, every forkful brings a delightful mix of flavors and textures that will surely make this recipe one of your favorites. Plus, it’s a subtle way to sneak in some veggies without sacrificing anything on taste.

Ingredients You'll Need

The image shows a close-up of a halved spaghetti squash placed on a white marbled surface. The squash has a pale yellow skin and the inside reveals a hollow cavity filled with light orange fibrous strands and several off-white seeds scattered around. The texture inside is stringy and slightly moist, with the thick pale yellow flesh surrounding the central cavity, completing the oval shape of the squash half. Parts of other squash halves are visible on the edges of the image. photo taken with an iphone --ar 4:5 --v 7

This Baked Spaghetti Squash and Cheese Recipe relies on simple, familiar ingredients that work together beautifully to create a rich and satisfying dish. Each component brings its own magic—from the mild cheddar’s creamy meltiness to the fresh pop of baby spinach, making every bite a perfect balance of comfort and nutrition.

  • Spaghetti squash: The star of the dish, acting as a healthy, low-carb pasta substitute with a naturally mild flavor and fun texture.
  • Butter and olive oil: These fats provide richness and help gently sauté the onions for a sweet depth of flavor.
  • Minced onion: Adds a subtle savory note that enhances the cream sauce base.
  • Flour (all-purpose or gluten-free): Essential for thickening the sauce and giving it that luscious, creamy consistency.
  • Skim milk: Keeps the sauce creamy without overwhelming heaviness, balancing richness and lightness.
  • Fat-free chicken or vegetable broth: Adds extra flavor to the sauce while keeping it lighter.
  • Reduced fat mild cheddar cheese: Melts wonderfully and rounds out the sauce with familiar cheesy goodness.
  • Salt and pepper: Simple seasonings to bring all the dish’s flavors into harmony.
  • Baby spinach: A healthy pop of bright green that wilts perfectly into the cheesy mixture without overpowering it.
  • Grated Parmesan: Sprinkled on top for a golden, slightly crunchy finishing touch.

How to Make Baked Spaghetti Squash and Cheese Recipe

Step 1: Prepare the Squash

Start by preheating your oven to 375ºF because we want everything nice and warm for our squash. Cut your spaghetti squash in half lengthwise and scoop out the seeds—think of it like prepping a little edible boat. Place the halves cut side down on a baking sheet and let them bake for about an hour until tender. Once cooked, use a fork to gently scrape out those beautiful spaghetti-like strands, which become the base of your dish. Don’t forget to squeeze out any excess moisture to keep everything creamy but not watery.

Step 2: Make the Creamy Cheese Sauce

While your squash is baking, melt butter with olive oil in a large saucepan over medium heat. Toss in the minced onion and sauté just until fragrant and translucent. Sprinkle in the flour and cook it gently for a few minutes, stirring constantly to cook out that raw flour taste—this forms the roux, the thickening backbone of your sauce. Slowly whisk in the milk and chicken broth, bringing the mixture to a gentle boil until it thickens beautifully. Season with salt and pepper, then stir in the mild cheddar cheese until it melts into a luxuriously smooth sauce.

Step 3: Combine and Bake

Now comes the fun part. Mix the cooked spaghetti squash strands and baby spinach into your creamy cheese sauce. The spinach will wilt gently from the warmth, adding color and a nutritional boost. Transfer everything into a baking dish and lavishly sprinkle grated Parmesan over the top. Pop it back into the oven for 25 to 30 minutes, until bubbly and golden on top—the cheese will form that irresistible crust that makes this dish so comforting.

How to Serve Baked Spaghetti Squash and Cheese Recipe

The image shows a white oval baking dish filled with a creamy, cheesy casserole that has a golden yellow top with melted cheese and small green herb pieces spread over it. The casserole looks thick with layers of melted cheese and cooked greens visible, and it has slightly browned edges where the cheese has baked. A silver spoon is scooping out a portion, held by a woman's hand, revealing the creamy and textured inside with bits of greens and cheese. In the background, there are white bowls with the same casserole and silver spoons inside them, all placed on a white marbled surface, giving a clean and bright look. photo taken with an iphone --ar 4:5 --v 7

Garnishes

To elevate your meal, try garnishing your dish with a little fresh chopped parsley or basil which adds brightness and a fresh contrast to the creamy richness. A light dusting of crushed red pepper flakes can also offer a subtle kick that wakes up the flavors beautifully. These small touches make it feel extra special.

Side Dishes

This recipe pairs wonderfully with a crisp green salad dressed in a tangy vinaigrette to balance out the cheesy richness. Roasted vegetables like asparagus or Brussels sprouts also complement it nicely by adding a satisfying texture and earthy notes. For a heartier meal, a crusty loaf of garlic bread is a fantastic choice to soak up any leftover sauce.

Creative Ways to Present

Looking to impress? Serve the Baked Spaghetti Squash and Cheese Recipe in individual ramekins for a charming presentation, perfect for dinner parties or family meals. You can also sprinkle some toasted breadcrumbs mixed with herbs over the Parmesan before baking to add a delightful crunch. For a twist, try layering it with thin slices of roasted tomato or sautéed mushrooms for extra flavor dimensions.

Make Ahead and Storage

Storing Leftovers

Once cooled, transfer any leftovers to an airtight container and keep them in the refrigerator for up to 4 days. The flavors actually deepen as it rests, making the next-day reheats even tastier. The texture might firm up a bit, but a quick reheat brings back the comfort perfectly.

Freezing

You can freeze this casserole for up to 2 months. Make sure to cool it completely before sealing it tightly in a freezer-safe dish or bag. Freeze in portions if you want easier meal prep for later. Thaw overnight in the fridge before reheating to keep the creamy sauce smooth and prevent separation.

Reheating

Reheat leftovers gently in the oven at 350ºF until warmed through to preserve the cheesy texture and avoid drying out. Microwave reheating works in a pinch, but stir halfway through and cover loosely to retain moisture and prevent the cheese from toughening.

FAQs

Can I use a different type of cheese in this recipe?

Absolutely! While the recipe calls for mild cheddar, feel free to swap in mozzarella for a stretchier texture, or a sharp cheddar for a bolder flavor. Gruyère or Monterey Jack also work beautifully if you want to mix things up.

Is this recipe suitable for vegetarians?

Yes, it is! Just swap the fat-free chicken broth with vegetable broth to keep it fully vegetarian-friendly without compromising flavor or creaminess.

How do I know when the spaghetti squash is fully cooked?

The best test is tenderness—poke the squash with a fork or knife after baking for about an hour. The flesh should be soft and easily separate into strands with a fork. If it’s still firm, give it a little more time in the oven.

Can I make this recipe gluten-free?

Definitely. Simply substitute the all-purpose flour with a gluten-free flour blend when making the roux. This swap will keep your sauce just as silky without any gluten concerns.

What can I serve with Baked Spaghetti Squash and Cheese Recipe for a balanced meal?

Pair it with a fresh green salad, some steamed or roasted veggies, and perhaps a light protein like grilled chicken or tofu for a well-rounded plate that complements the cheesy squash dish perfectly.

Final Thoughts

There’s something so wonderfully comforting about this Baked Spaghetti Squash and Cheese Recipe that you’ll want to make it again and again. It’s cheesy, wholesome, and surprisingly easy to pull together, making it an ideal weekday dinner or a crowd-pleasing side. Give it a try soon—you might just discover your new favorite way to enjoy spaghetti squash!

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Baked Spaghetti Squash and Cheese Recipe

Baked Spaghetti Squash and Cheese Recipe

5 Stars 4 Stars 3 Stars 2 Stars 1 Star 4 from 47 reviews
  • Author: Ivy
  • Prep Time: 20 minutes
  • Cook Time: 1 hour 25 minutes
  • Total Time: 1 hour 45 minutes
  • Yield: 7 servings
  • Category: Main Dish
  • Method: Baking
  • Cuisine: American
  • Diet: Low Fat
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Description

This Baked Spaghetti Squash and Cheese recipe offers a comforting, lighter alternative to traditional pasta dishes. Featuring tender roasted spaghetti squash strands mixed with a creamy, cheesy sauce enriched with spinach, this casserole is baked to golden perfection for a wholesome, satisfying meal that's perfect for family dinners or meal prepping.


Ingredients

Main Ingredients

  • 5 ½ cups cooked spaghetti squash (from about 2 small squash)
  • 1 tbsp butter
  • 1 tbsp olive oil
  • ¼ cup minced onion
  • ¼ cup flour (use all-purpose gluten-free flour for gluten-free option)
  • 2 cups skim milk
  • 1 cup fat free chicken broth (or vegetable broth for vegetarian)
  • 2 cups (8 oz) Sargento 2% reduced fat mild cheddar, shredded
  • Salt and pepper, to taste
  • 4 cups (about 4 oz) baby spinach
  • ⅛ cup grated parmesan cheese


Instructions

  1. Preheat Oven: Preheat your oven to 375ºF (190ºC) to prepare for baking the spaghetti squash.
  2. Prepare Spaghetti Squash: Cut the squash in half lengthwise and remove and discard the seeds. Place the squash halves cut side down on a baking sheet and bake for about 1 hour, until the flesh is tender and easily strands with a fork.
  3. Shred Squash: Using a fork, scrape to separate the strands of cooked squash and transfer to a medium bowl. Discard the squash shells. If the squash appears watery, squeeze out the excess liquid gently to avoid sogginess in the final dish.
  4. Maintain Oven Temperature: Keep the oven set at 375ºF to bake the assembled casserole later.
  5. Sauté Onion: In a large saucepan over medium heat, melt the butter and olive oil. Add the minced onion and cook for about 2 minutes until softened and fragrant.
  6. Make Roux: Stir in the flour to the onion mixture, reduce heat to low, and cook while stirring continuously for 3 to 4 minutes to remove the raw flour taste and form a thick base.
  7. Add Liquids and Thicken Sauce: Gradually whisk in the skim milk and chicken broth, increase heat to medium-high, and continue whisking until the sauce comes to a boil and thickens, approximately 2 minutes. Season with salt and pepper to taste.
  8. Add Cheese: Remove the saucepan from heat and stir in the shredded cheddar cheese until fully melted and the sauce is smooth and creamy.
  9. Combine Ingredients: Adjust seasoning if needed, then fold the cooked spaghetti squash strands and baby spinach into the cheese sauce. Transfer the mixture into a baking dish and evenly sprinkle grated parmesan cheese over the top.
  10. Bake Casserole: Bake in the preheated oven for 25 to 30 minutes until the dish is bubbly and the top is golden brown, indicating it’s cooked through and deliciously cheesy.

Notes

  • For a vegetarian version, substitute chicken broth with vegetable broth.
  • To make the dish gluten-free, use gluten-free flour instead of all-purpose flour.
  • Squeezing out excess moisture from the cooked spaghetti squash helps prevent the casserole from becoming soggy.
  • This recipe serves 7, making it perfect for meal prep or family meals.
  • Feel free to add herbs like thyme or basil for extra flavor.

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Hey, I’m Ivy!

I’m a 28-year-old mom to my little prince, Pitter, who loves cooking and exploring flavors from around the world. What started in my home kitchen is now a space where I share simple, global-inspired recipes made with love.

 

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