If you are looking for the ultimate comfort food that won’t weigh you down, this is it. This vegan baked spaghetti squash recipe transforms a simple vegetable into a bubbling, savory, and cheesy-tasting casserole.
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It is packed with organic spinach, bright marinara sauce, and savory nutritional yeast. It’s the perfect plant-based dinner that satisfies that deep craving for a “pasta bake” without any of the gluten or dairy.
This dish is vibrant, healthy, and surprisingly easy to pull together for a cozy weeknight meal.
A Little Story About This Dish
I used to think of spaghetti squash merely as a plain side dish, something you served with a little butter and salt. But one evening, craving a hearty lasagna but wanting to keep things light, I decided to experiment.
I scraped out those tender, noodle-like strands and tossed them with my favorite red sauce and greens, then baked it all again like a casserole. The result was magic.
This specific spaghetti squash recipe has become my secret weapon. It feels indulgent and rich, yet it’s entirely plant-based and packed with nutrients. It’s the dish that finally made me fall in love with squash.
Get Ready to Cook!
You are just a few steps away from a healthy, “cheesy,” and delicious pasta alternative. Let’s look at what you need to get started.
What to Expect
Time: Approximately 1 hour and 15 minutes (mostly hands-off baking time).
Difficulty: Very easy! The oven does almost all the work.
Before You Begin
The most important step is properly roasting the squash first. Roasting it cut-side down traps the steam, creating perfectly tender “noodles.”
For this recipe, we use a “flax egg” as a binder. This mixture of ground flax seeds and water helps hold the casserole together, giving it a great texture similar to a traditional pasta bake.
Finally, don’t skip the broil step at the end! That high heat gives the top a delightful crispy texture that contrasts beautifully with the tender interior.
The Heart of the Dish: Ingredients You’ll Need
Here are the wholesome ingredients for this vegan baked spaghetti squash recipe.
| Ingredient | Amount |
| For the Squash: | |
| Organic Spaghetti Squash | 1 (medium-large) |
| Himalayan Pink Salt & Black Pepper | To taste |
| For the Flax Egg: | |
| Organic Ground Flax Seeds | 1 tablespoon |
| Filtered Water | 2 tablespoons |
| For the Add-Ins: | |
| Organic Baby Spinach, diced in strips | 3 cups |
| Organic Marinara Sauce (citric acid-free) | 1 cup |
| Nutritional Yeast (optional, for cheesy flavor) | ½ cup |
| Organic Garlic, fresh crushed | 3 cloves |
| Ground Cayenne Pepper | ½ teaspoon |
| Himalayan Pink Salt | ¼ teaspoon |
| For Garnish: | |
| Fresh Basil Leaves, sliced | Handful |
Let’s Get Cooking! Step-by-Step Guide
Follow these simple steps to create this comforting vegetable-packed casserole.
1. Prep the Oven and Squash:
Preheat your oven to 350°F (175°C). Line a cookie sheet with parchment paper and have an 8×8 baking dish ready. Carefully cut the spaghetti squash in half lengthwise and scrape out the seeds. Sprinkle the insides with a pinch of pink salt and pepper.
2. Roast the Squash:
Place the squash halves face down on the lined cookie sheet. Bake for about 45-50 minutes. You want the flesh to be tender. Once cooked, use a fork to scrape the strands out, creating your “spaghetti” noodles.
3. Make the Flax Egg:
While the squash roasts, whisk together the ground flax seeds and 2 tablespoons of water in a small bowl. Set it aside for a few minutes to thicken.
4. Assemble the Mixture:
In a medium mixing bowl, combine the cooked spaghetti squash strands with the spinach, marinara sauce, nutritional yeast, crushed garlic, cayenne pepper, and the ¼ teaspoon of salt. Give the flax egg another whisk and pour it into the bowl. Gently toss everything together until it is well combined.
5. Bake the Casserole:
Transfer the squash mixture into your 8×8 baking dish. Increase the oven temperature to 375°F (190°C) and bake for 10-15 minutes until warmed through.
6. Broil and Serve:
Switch your oven to the broil setting. Let the dish broil for about 5 minutes, watching closely, until the top gets a little crispy and golden. Garnish with fresh chopped basil strips and serve hot!
Mastering the Dish: Pointers for Perfection & How to Store
Here are a few extra tips to make your spaghetti squash bake incredible.
Pointers for Perfection
If you want a spicier kick, increase the cayenne or add red pepper flakes. If serving to kids, feel free to omit the spice entirely. Nutritional yeast provides that savory, cheesy flavor without dairy, but you can skip it if following strict dietary protocols.
How to Store
This dish reheats wonderfully. Store leftovers in an airtight container in the refrigerator for up to 4 days. You can reheat it in the oven or microwave until warm.
For those in search of new gluten-free meal ideas, these recipes are a great source of inspiration: Gluten Free hamburger casserole, and Ground Beef Enchilada Skillet, and The Best Gluten-Free Lemon Chicken Pasta.
Your Burning Questions Answered!
Here are answers to some common questions about cooking with spaghetti squash.
1. Does spaghetti squash have gluten in it?
No, spaghetti squash is a vegetable and is naturally 100% gluten-free. It is a fantastic alternative to wheat-based pasta for those with Celiac disease or gluten sensitivities, providing a similar texture without the grains.
2. What’s the trick to cooking gluten-free pasta?
While this recipe uses squash as the “pasta,” if you substitute it with actual gluten-free pasta noodles, the trick is not to overcook them. Gluten-free pasta can get mushy quickly. Cook it in plenty of salted water, taste it a minute before the package says it’s done, and rinse it with cool water immediately after draining to stop the cooking process.
3. What seasonings are good on spaghetti squash?
Spaghetti squash has a very mild, slightly sweet flavor that pairs well with almost anything. Italian seasonings like basil, oregano, and garlic are classic choices. However, it also works great with tex-mex flavors like cumin and chili powder, or simply tossed with olive oil, salt, and nutritional yeast.
Dig In & Enjoy!
You are ready to enjoy a vibrant, healthy meal that feels like a cheat day. Enjoy every bite of this wholesome spaghetti squash recipe!
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The Best Gluten Free Baked Spaghetti Squash Recipe
- Total Time: 1 hour 15 minutes
- Yield: 4 servings 1x
Description
A comforting and healthy vegan baked spaghetti squash recipe! This casserole-style dish combines tender squash noodles with savory marinara, spinach, and nutritional yeast for a cheesy, dairy-free finish. Perfect for a gluten-free dinner.
Ingredients
1 organic spaghetti squash (medium-large)
1 tablespoon organic ground flax seeds
2 tablespoons water (filtered/purified)
3 cups organic baby spinach (diced in strips)
1 cup organic marinara pasta sauce (citric acid-free)
½ cup nutritional yeast (omit to be 100% Medical Medium® compliant)
3 cloves organic garlic (freshly crushed)
½ teaspoon organic ground cayenne pepper
¼ teaspoon Himalayan pink salt
Black pepper to taste
Fresh basil leaves (for garnish)
Instructions
1. Preheat oven to 350°F (175°C). Line a cookie sheet with parchment paper and prepare an 8×8 baking dish.
2. Cut the spaghetti squash in half lengthwise and scrape out the seeds. Sprinkle the insides with a pinch of pink salt and black pepper.
3. Place squash halves face down on the cookie sheet. Bake at 350°F for 45-50 minutes. Once done, scrape the inside strands out with a fork.
4. Make the flax egg: Whisk together flax seeds and water in a small bowl and set aside.
5. In a medium bowl, combine the cooked squash strands, baby spinach, marinara sauce, nutritional yeast, garlic, cayenne pepper, and salt.
6. Add the flax egg to the bowl and gently toss until all ingredients are well combined.
7. Transfer the mixture to the 8×8 baking dish. Increase oven heat to 375°F (190°C) and bake for 10-15 minutes until warmed through.
8. Switch oven to broil and cook for 5 minutes until the top is crispy. Garnish with fresh basil and serve hot.
Notes
Serving Size: One medium-large squash yields about 4 servings.
Substitutions: You can use organic garlic powder instead of fresh garlic, and red pepper flakes instead of cayenne.
Make it Cheesy: The nutritional yeast adds a savory, cheese-like flavor without dairy. Omit for Medical Medium compliance.
- Prep Time: 10 minutes
- Cook Time: 1 hour 5 minutes
- Category: Main Course, Dinner
- Method: Baking, Roasting
- Cuisine: American, Italian-Inspired
Nutrition
- Serving Size: 1 1/2 cups
- Calories: 129
- Sugar: 9g
- Sodium: 526mg
- Fat: 3g
- Saturated Fat: 0g
- Unsaturated Fat: 0g
- Trans Fat: 0g
- Carbohydrates: 24g
- Fiber: 7g
- Protein: 6g
- Cholesterol: 0mg