This Mediterranean spaghetti squash bake is one of our favorite ways to enjoy winter squashes. With layers of spaghetti-like strands, vibrant veggies, and the option for a cheesy or crunchy topping, it's a cozy vegetarian main course you’ll want to make on a regular basis.
Favorite spaghetti squash recipes
After returning from India, I found myself drawn to the grocery stores, lured by the bins of bright, freshly harvested winter squashes.
That’s how I knew fall had officially arrived. For me, it’s the season of bakes and braises—of roasting, layering, and turning on the oven not just for warmth, but for comfort.
This spaghetti squash bake is rooted in that feeling.
I grew up loving a simple side dish of baked squash with butter, salt, black pepper, and a bit of Parmesan cheese—a recipe passed down from my grandmother, Anne Ell.
Now I’ve taken that idea and layered it with Mediterranean flavors to make one of my absolute favorite spaghetti squash recipes.
Jump to:
- Favorite spaghetti squash recipes
- Cooking spaghetti squash
- Little story behind the recipe
- Why you'll love this recipe
- Get your FREE cookbook!
- Ingredients
- Helpful equipment
- Step-by-step instructions
- Variations & Tips
- How to store and reheat
- Have you tried this recipe?
- Recipe for Mediterranean Spaghetti Squash Bake
- More recipes you may enjoy
- Tried this recipe? We’d love your review!
Cooking spaghetti squash
The beauty of this dish lies in its simplicity. It starts with squash halves, which you steam to create those soft spaghetti-like strands that make this vegetable feel like spaghetti noodles—but lighter, healthier, and more interesting.
From there, you layer on a savory mix of zucchini, red bell pepper, onions, garlic, and optionally, tomatoes or eggplant.
The bottom layer is seasoned with ghee, cumin, and black pepper to bring out the best flavor.
The top? Your choice: go cheesy, crunchy, or keep it rustic and veggie-focused.
This is a great way to turn a large squash into a meal that’s satisfying and packed with vegetables.
It’s also a perfect texture contrast between the soft squash base and the roasted topping.
The result is golden brown, bubbling, and exactly the kind of food that belongs in the center of your fall table.
Little story behind the recipe
I’ve always had a soft spot for dishes that require just a little bit of effort but pay off in a big way. That’s this recipe.
It's simple enough for a weeknight, yet beautiful and flavorful enough for company.
Honestly, one of the hardest parts is cutting the squash. You’ll need a very sharp chef’s knife, a sturdy cutting board, and a steady hand.
Start from the stem end and slice downward on a flat surface.
Once steamed, you’ll scoop out the inside of the squash using a large spoon, watching it fall into those tender, spaghetti-like strands that make this dish so visually fun and so texturally satisfying.
Why you'll love this recipe
By the end of this, you’ll know the best way to steam squash (no roasting necessary!), how to balance veggies with spices, and how to assemble a perfectly layered baking dish using simple ingredients.
You’ll also learn the differences between steaming on the stove versus using an Instant Pot, and how to store leftovers in an airtight container for easy reheating.
Whether it’s your first time cooking spaghetti squash, or you're just looking for new favorite recipes, this dish has you covered.
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Ingredients
Let’s break down what you’ll need:
- Spaghetti squash – The base of the dish, steamed and scooped later
- Potatoes – Or swap for sweet potato or taro root for a nightshade-free version
- Zucchini – Adds moisture and fresh texture
- Tomatoes, red bell pepper, or eggplant – Adds color and flavor (or use carrots if avoiding nightshades)
- Onions and garlic – The foundation of the topping
- Fresh oregano – Earthy and Mediterranean
- Cumin powder, salt, black pepper – Essential flavoring for the squash base
- Ghee – Or a little olive oil for richness
- Optional: Parmesan cheese, feta cheese, cheddar, or chopped almonds
All of these ingredients can be found at your local grocery store, and they come together effortlessly in one baking dish.
Helpful equipment
Here’s what makes the process smoother:
- Large saucepan with steamer insert, or Instant Pot with trivet
- Large bowl and medium mixing bowl
- 8x11 roasting dish or baking dish
- Very sharp chef’s knife and cutting board
- Large spoon for scooping the squash
These tools help speed up prep and ensure the perfect texture in your finished bake.
Step-by-step instructions
Steam the squash and potatoes
Slice off the stem end, then cut the squash upright in half. Place the squash halves and halved potatoes cut-side-down in your steamer. Steam until a knife glides in easily.
Chop your topping ingredients
In a large bowl, mix chopped zucchini, red pepper, onions, garlic, and any additional vegetables. Add steamed potato, olive oil, salt, and pepper.
Prepare the squash layer
Once the squash is cool, remove seeds with a large spoon. Scrape out the spaghetti-like strands into your medium mixing bowl and mix with ghee, salt, cumin powder, and black pepper.
Assemble the bake
Spread the squash mixture into your baking dish. Layer the vegetable topping evenly. Cover with foil.
Bake it
Bake at 375°F for 25 minutes, then uncover and continue baking for 15 minutes, or until the top is golden brown.
Add your topping
Finish with Parmesan cheese or chopped almonds, and bake just a few more minutes until bubbly and crisp.
Variations & Tips
- Want to make it nightshade-free? Skip the tomatoes and red pepper. Use carrots or stick with squash and zucchini.
- Want extra protein? Serve with lentils, mung dal, or canned chickpeas.
- Want it crispier? Sprinkle almonds on top before baking uncovered.
For the best results, make sure your squash is fully cooked and not watery. Use a sharp knife, and let everything cool slightly before handling.
How to store and reheat
Cool leftovers completely and store in an airtight container. Reheat in the oven or toaster oven for best texture.
You can also freeze individual portions if you want to prep a large batch in advance.
This Mediterranean spaghetti squash bake is one of those favorite recipes that feels both grounding and fresh.
It's nourishing, adaptable, and a great way to enjoy the changing seasons without fuss.
Whether you’re using acorn squash, experimenting with zucchini noodles, or just want to learn the basics of cooking squash, this is a recipe that teaches you how to work with simple ingredients while getting great results.
Have you tried this recipe?
Did you try this? Was it your first time cooking spaghetti squash? Share your thoughts below!
And while you're here, check out more of my fall and winter recipes like this Vegan Butternut Squash Mac and Cheese, Butternut Squash Soup, and Baked Butternut Squash and Leeks. And don’t miss the Butternut Squash and Fennel Root Soup—it’s pure comfort in a bowl.
Save this one, print the recipe card, and let it be your go-to for those chilly nights when only something warm and veggie-packed will do.
Recipe for Mediterranean Spaghetti Squash Bake
Helpful Kitchen Tools:
- large saucepan with a steamer and lid OR Instant Pot with basket or trivet
- large mixing bowl (for the topping)
- medium mixing bowl (for the squash)
Ingredients
to steam
- 1 medium spaghetti squash
- 2 medium potatoes, (sub with sweet potato or taro root)
for the vegetable topping
- 2 cups zucchini
- 2 cups tomatoes and/or eggplant and/or red bell pepper, (see notes for substitution)
- ½ cup onion
- 1 clove garlic, (sub with cilantro, parsley, basil, etc.)
- 1 teaspoon salt
- ¼ teaspoon freshly ground black pepper
- 1 tablespoon olive oil
for the squash flavor
- 1 tablespoon ghee
- ½ teaspoon salt
- ½ teaspoon cumin powder
optional toppings
- cheddar (grated), feta cheese (crumbled), or Parmesan
- almonds, roughly chopped
Instructions
To steam the squash and potatoes
- Add 1 cup water to your saucepan or Instant Pot. Insert steamer basket or trivet.
- Slice off the stem and root ends from the spaghetti squash, then slice in half lengthwise. Place cut side down on the steamer basket.
- Slice potatoes in half lengthwise and place cut side down on the steamer basket.
- For the saucepan, bring water to a boil, then reduce the heat and simmer/steam for 20 minutes. The squash is ready when a knife inserted into the squash comes out easily when lifted. For the Instant Pot, select “STEAM” and set the timer for 12 minutes. Manually release the steam after 5 minutes and open the lid.
For the vegetable topping
- Meanwhile, assemble the rest of the ingredients in a large mixing bowl. Chop zucchini, tomatoes, eggplant, and/or red pepper into small pieces of about ½-inch in diameter. Chop onions, garlic, and oregano even finer.
- After the potatoes are cool enough to handle, chop them into ½-inch pieces and add to the mixing bowl.
- Add salt, black pepper, and olive oil, and mix well. Taste a potato for salt. Add more salt if needed. If you didn’t use any tomatoes, add a bit of lemon juice. Set aside.
Finish the squash and assemble the bake
- Preheat the oven to 375 degrees Fahrenheit.
- After the spaghetti squash is cool enough to handle, use a large serving spoon to scoop the seeds out and discard. Now scoop the spaghetti flesh out and place in your medium mixing bowl.
- Mix in ghee, salt, pepper, and cumin powder.
- Transfer to the baking tray and spread evenly over the bottom. Add the prepared vegetable topping and spread evenly. Cover with aluminum foil
- Place in the oven. Bake for 25 minutes, then remove the covering. Continue to bake until the veggies are browning on top (about 15 minutes).
- Add optional cheese or nuts and bake a few minutes more until the cheese is bubbly and the nuts are golden.
Video
Notes
Nutrition
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