Microwave spaghetti squash is a quick, simple, and fuss-free way to cook this low carb pasta alternative at home! 

A fork is scooping some spaghetti squash cooked in the microwave. The red banner at the bottom reads paleo, Whole30, low carb, gluten-free, and vegan

The original healthy pasta alternative!

Before spiralized zucchini (a.k.a. zoodles) was all the rage as the low carb and keto-friendly alternative for pasta, the lowly spaghetti squash was the only pasta substitute in town.

And you know what? Sometimes the original is the best! Although no one would ever mistake these slightly squeaky and neutral tasting vegetable strands as the real thing, cooked spaghetti squash is a great vehicle for hearty pasta sauces and will scratch that noodle itch!

An overhead view of spaghetti squash cooked in the microwave and shredded with a fork.

What is the best way to cook spaghetti squash?

I’ve tested various methods for cooking spaghetti squash—from slow cooking and baking to pressure cooking and microwaving. I’m the queen of shortcuts to deliciousness, so any method that takes longer than 30 minutes, like slow cooking or roasting in the oven, is out in my book.

As a result, we’re left with microwaving or pressure cooking in the Instant Pot, two fantastic methods to cook spaghetti squash quickly, easily, and without heating up the kitchen.

I love my Instant Pot spaghetti squash, but sometimes it’s already filled with another dish. That’s when I turn to my microwave!

Two hands are placing a glass bowl filled with a halved spaghetti squash into an open microwave

Is it safe to cook food in the microwave?

I know many people have reservations about cooking food in the microwave because they’ve heard that microwave cooking destroys nutrients or the microwave itself is unsafe. However, from the research I’ve read, I’ve concluded that microwave cooking is safe so I use it regularly.

If you’d like to read more about why microwaves are safe for cooking, here’s a great article by Paleo Mom and another one by the smarties at Harvard Medical School. If you’re still unconvinced, you can simply use my Instant Pot method!

What is the best way to cut spaghetti squash?

The best way to cut spaghetti squash is to use a sharp knife and cut it crosswise through the center so you end up with long strands of “noodles.”

A spaghetti squash cut in half crosswise with the seeds exposed.

The flesh of the spaghetti squash runs in concentric rings around the center so when you cut it lengthwise, you end up with short strands. Obviously, if you don’t care about the length of the strands, you can cut it any which way you like!

Although some people recommend microwaving the whole squash (after pricking the skin a few times) to make it easier to cut, I find a sharp paring knife does the trick without taking that extra step. Plus, you don’t run the risk of the squash exploding in the microwave if you didn’t pierce it properly.

I know some of you will ask whether you can cook the whole squash in the microwave without cutting it, and my answer is: NO. Even when I pierce it adequately to ensure it doesn’t explode in the microwave, I find the end result unsatisfactory—the squash is either too soft or cooked unevenly.

What size spaghetti squash should I use?

I like to pick smaller squash, about 2 pounds each, because the halved squash fit nicely in my Large Deep Dish Anyday bowl and half a squash is the right serving size for me. If you have a larger squash, you can cut them into rings that are about 2-inches thick and follow the same instructions below.

A smiling Asian woman is holding a small spaghetti squash and a large deep Anyday microwave bowl.

The best microwave dishes to use

Even though cooking in the microwave is a safe, microwaving food in plastic is not healthy because chemicals in the container can transfer or leak into your food. That’s why I only use glass containers when I microwave these days.

Recently, I discovered a line of microwaveable containers that I’ve come to love, Anyday bowls. I first learned about them from Chef David Chang’s Instagram posts; as soon as I saw all the fast and easy dishes he was whipping up with them, I was intrigued.

Someone in a red apron is holding a round Anyday microwave glass container.

I bought my first set and tried it out. After successfully steam-cooking veggies and chicken in the microwave with my glass Anyday bowls, I was hooked. For this recipe, I use the large deep dish size or the extra large dish to microwave spaghetti squash.

As many of you know, when I discover a product I like, I become a crazy evangelist. I start proselytizing so fervently that people assume I’m a paid shill for products like the Instant Pot—but that’s not the case. I kind of just get carried away, which is why you’ll probably hear me talking up Anyday from here on out. (It’s not a paid sponsor but I am an affiliate if you buy them through this link. Also, save 10% off with code: NOMNOMPALEO)

You can learn more about why Anyday bowls are awesome in my Crispy Microwave Bacon post. (Yes, you can use them to make crispy bacon!)

Don’t have Anyday bowls? You can also use a lidded glass baking dish, like CorningWare, or a microwave safe glass bowl and a silicone lid. However, the Anyday bowls steam everything more evenly because of their unique vented lids.

How to make spaghetti squash in the microwave

Cut the spaghetti squash in half crosswise

Use a sharp paring knife to cut the spaghetti squash in half crosswise. If you have a large spaghetti squash, cut it crosswise into 2-inch thick rings.

A person in a red apron is using a sharp paring knife to cut a small spaghetti squash in half crosswise in the middle.

Remove the seeds

With a large spoon, scrape out the seeds in the center of the squash. You can discard the seeds or roast them in the the oven like pumpkin seeds.

A spaghetti squash is cut in half crosswise and the seeds have been scooped out and discarded

Place the squash in a microwave-safe glass container

Put half of the squash in a microwave-safe dish and add two tablespoons of water.

Someone in a red apron is adding a spoonful of water to a glass container with a half of a spaghetti squash inside

Cover the container

Place a lid on the container making sure to leave a small vent. A microwave-safe silicone lid works well if your glass container doesn’t come with a lid.

Placing a lid on a glass container with half a spaghetti squash inside.

Microwave for 8 to 12 minutes

The amount of time it takes to cook in the microwave can vary depending on the wattage, but the total cook time is about 8 to 12 minutes for the strands to easily come away from the skin when scraped with a fork.

A fork is scraping the microwave spaghetti squash away from the skin.

I have a 1200 watt microwave and it takes about 9 minutes for the spaghetti squash to be the way I like it, which is still a little toothsome and al dente. Start checking at 7 minutes and continue cooking at 1 minute or 30 second intervals until it is the desired consistency. Also, if you’re cooking the spaghetti squash for future meals, you can err on the al dente side because you’ll continue cooking it later.

Taking the lid off a glass bowl and checking on the spaghetti squash.

Cool for 5 minutes and scrape the spaghetti squash strands out with a fork. Repeat the same steps to cook the other half of the squash.

An overhead shot of a spaghetti squash cut in half crosswise with the cooked strands resembling long noodles.

Season the microwave spaghetti squash

Spaghetti squash has a naturally bland flavor after you cook it (similar to pasta), so season it to taste with salt and freshly ground black pepper (or your favorite Nom Nom Paleo seasoning blend!) Then, top it with your favorite sauce!

How do you store and reheat microwave spaghetti squash?

Cooked spaghetti squash can be kept in the fridge for up to 4 days in a sealed container. You can reheat the spaghetti squash in a covered and vented microwave-safe dish for about 45 to 90 seconds or until heated through. Alternatively, you can sauté the spaghetti squash in a frying pan over medium heat with a little extra virgin olive oil until heated through.


Looking for more recipe ideas? Head on over to my Recipe Index. You’ll also find exclusive recipes in my cookbooks, Nom Nom Paleo: Food for Humans (Andrews McMeel Publishing 2013), Ready or Not! (Andrews McMeel Publishing 2017), and Nom Nom Paleo: Let’s Go! (Andrews McMeel Publishing 2022).


PRINTER-FRIENDLY RECIPE CARD

Microwave Spaghetti Squash

4.80 from 10 votes
Prep Time5 minutes
Cook Time9 minutes
Cooling Time10 minutes
Total Time24 minutes
Servings 2
Microwave spaghetti squash is a quick, simple, and fuss-free way to cook this low carb pasta alternative at home! 

Ingredients 
 

Instructions 

  • Use a sharp paring knife to cut the spaghetti squash in half crosswise.
  • With a large spoon, scrape out the seeds in the center of the squash. You can discard the seeds or roast them like pumpkin seeds.
  • Put half of the spaghetti squash in a microwave-safe glass container and add two tablespoons of water. Place a lid on the container making sure to leave a small vent. A microwave-safe silicone lid works well if your glass container doesn’t come with a lid.
  • The amount of time it takes to cook in microwave can vary depending on the wattage, but the total cook time is about 8 to 12 minutes for the strands to easily come away from the side when scraped with a fork.
    For a 1200 watt microwave, it takes about 9 minutes for the spaghetti squash to be a little toothsome and al dente. Start checking at 7 minutes and continue cooking at 1 minute or 30 second intervals until it is the desired consistency. Also, if you’re cooking the spaghetti squash for future meals, you can err on the al dente side because you’ll continue cooking it later.
  • Cool for 5 minutes and scrape the noodles out with a fork. Repeat the same steps to cook the other half of the squash.
  • Season the spaghetti squash with salt and pepper to taste.

Video

Notes

Nutrition

Calories: 100kcal | Carbohydrates: 22g | Protein: 2g | Fat: 2g | Fiber: 5g | Sugar: 9g

Nutrition information is automatically calculated, so should only be used as an approximation.

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About Michelle Tam

Hello! My name is Michelle Tam, and I love to eat. I think about food all the time. It borders on obsession. I’ve always loved the sights and smells of the kitchen. My mother was (and is) an excellent cook, and as a kid, I was her little shadow as she prepared supper each night. From her, I gained a deep, abiding love for magically transforming pantry items into mouth-watering family meals.

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