Spaghetti Squash Meal Prep (Easy, High-Protein, Whole30)
Bringing back this oldie but goodie post, I can’t believe this recipe was created so long ago in the midst of Covid. With the temps dropping during this time of the year, I found myself craving a cozy and hearty meal, and this one totally hit the spot. If you have never tried spaghetti squash before, this is a great recipe to start with. So easy to make and can be prepped in bulk for the whole family to enjoy.
If you are new in the blog, you should know that I love to meal prep. I have been meal prepping for years as it is very convenient when you have a full-time job, other life responsibilities and are trying to eat healthy. I cannot emphasize enough the amount of mental stress meal prep relives as I don’t have to think about what to eat every day. Everything is already planned and prepared.
These Spaghetti Squash bowls are perfect for meal prep and super versatile as they can be customized to your taste.
This post may contain affiliate links, which means that I make a small commission off items you purchase at no additional cost to you.

Why You’ll Love This Spaghetti Squash Meal Prep
This meal checks all the boxes for busy weeks:
- High-protein, easy customizable with beef, chicken, turkey, or beans
- Budget friendly
- Quick weeknight meal for the whole family
- Great to stay on track on your healthy eating journey
- Only made with whole food ingredients – Whole 30 friendly with easy swaps
- Stores well for 4 days
- Comforting, filling and very tasty
Ingredients
To meal prep these Spaghetti Squash Bowls you’ll need:
- 1 medium spaghetti squash
- 1 lb ground turkey or beef
- 1 jar of tomato sauce (I used Rao’s)
- Fresh mozzarella
- Fresh basil
- 1 medium yellow onion
- 2 cloves of garlic
- Mushrooms (optional)
How to Make Spaghetti Squash Meal Prep
Let’s walk-through how to meal prep spaghetti squash step-by-step.
Bake the Spaghetti Squash
First, preheat the oven to 400 degrees and prep a baking sheet with parchment paper.
Start by roasting the spaghetti squash. Cut the squash into two equal halves lengthwise and scoop out the seeds with a metal spoon. Spray or brush the inside of each half with olive oil, then sprinkle with salt and pepper. Turn the spaghetti squash halves over so they are face-down and place them on the baking sheet skin side up.
Cover the baking sheet with foil to help retain moisture and transfer to the pre-heated oven. Roast for 45-60 minutes. To check if the spaghetti squash is cooked, pierce the top with a fork or gently press down. this should be soft.
Next, remove the baking sheet from the oven, uncover the spaghetti squash and let it cool down. When cool, shred the inside of the spaghetti squash with a fork by running it lengthwise.

Make your Protein
While the spaghetti squash bakes in the oven make your protein or the topping of your choosing. In this case, I’ll walk you step-by-step on how to prep the ground turkey or beef. First, dice your onion and mince your garlic. Add a drizzle of olive oil in a pan and heat over medium heat. When hot, add the onion and garlic. Sauté for 1-2 minutes or until fragrant. Add your mushrooms (if using) and sauté for another 2 minutes.
Finally, add your meat, season with salt and pepper and break up with the back of a spoon. Cook until meat is cooked through or no longer pink, about 5-7 minutes. Drain-off the excess fat.
Reduce heat to simmer and pour your tomato sauce. Cook for another 10 minutes.
Assemble Spaghetti Squash Bowls
When the spaghetti squash and meat sauce are ready, assemble your containers. Make sure your containers are glass and oven safe. Evenly divide the spaghetti squash and meat sauce in 4 portions. First, add the squash at the bottom of the containers to form a thick layer, then top with the meat sauce. Add sliced mozzarella
Transfer your containers to a pre-heated oven and bake for 10-15 minutes, or just long enough to melt the cheese. Remove from the oven and top with fresh basil.

Spaghetti Squash Bowls Variations
As mentioned before this meal is very versatile and you can add your own ingredients to make it your own.
High-Protein Version
You can swap the ground turkey or beef for whatever type of protein your heart desires. Other high-protein versions of this meal include:
- Shredded chicken and tomato sauce – if very tight on time you could use rotisserie chicken for this version
- Ground chicken and tomato sauce
- Turkey or ground beef meatballs with your sauce of choice – tomato sauce is recommended
- Add an egg
Vegan Version
- Add chickpeas
- Add beans
- Sauteed mushrooms and marinara
- Roasted broccoli and parmesan
- Tofu
Spaghetti Squash Bowls Storage and Reheating
You can store these Spaghetti Squash Bowls up to 4 days in the fridge. These are the glass containers I use. You might be able to store them a little longer, but it’s not recommended to maintain freshness. To extend the life, you can store them in the freezer. However, please note that I haven’t tried freezing these bowls so I can’t guarantee the flavor nor texture.
To re-heat simply microwave for 1 minute or use a toaster oven in the warm setting.
If you are new to meal prepping, this recipe is great as it doesn’t involve too many ingredients or complicated steps. I hope you give these Spaghetti Squash Bowls a try. Let me know if you try it in the comments. Enjoy!
Spaghetti Squash Meal Prep Recipe FAQs
🌿 How do I store spaghetti squash meal prep?
You can store it in airtight glass containers for up to 4 days in the refrigerator.
🌿 How long does spaghetti squash meal prep last?
This meal prep can easy last 4-5 days. Long enough for an entire work week.
🌿 Can I freeze spaghetti squash meal prep?
I never tried freezing this meal, the texture of the squash might not be the best after frozen. However, if you decide to freeze, I recommend you label and date the containers/bags before placing in the freezer and also recommend using within 1 month.
🌿 How do I reheat/use frozen spaghetti squash bowls?
Although I never tested this before, I would recommend transferring the containers/bags to the refrigerator and let it thaw overnight. Reheat in an oven-safe dish in the oven for 30 -40 minutes or until meat is heated through.

Spaghetti Squash Bowls Meal Prep
Ingredients
Method
- Preheat oven to 400 deg.
- Cut spaghetti squash in half, lengthwise. Scoop out the seeds with a metal spoon,
- Brush of spray the inside of each half with olive oil and sprinkle with salt and pepper.
- Place spaghetti squash halves (skin side up) onto a baking sheet lined with parchment paper.
- Cover baking sheet with aluminum foil.
- Place in the oven and bake for 45-60 minutes. Squash should be soft to the touch, try piercing with a fork.
- When the squash is ready, remove from oven and let it cool down.
- Meanwhile, while the squash bakes in the oven, prep your meat sauce. Start by dicing the onion.
- Mince the garlic.
- Heat olive oil in a skillet over medium high heat. When hot, add diced onion and garlic and cook until fragrant, 1-2 minutes.
- Add the mushrooms (if using) and cook for another 2 minutes.
- Add ground turkey/beef, break meat with the back of a spoon. Season with salt and pepper and cook until no longer pink, 5 to 7 minutes.
- Reduce heat to simmer and add tomato sauce. Cook for 10-15 minutes.
- Using a fork shred the spaghetti squash and divide into 4 even portions.
- Distribute the spaghetti squash among the containers by forming a thick layer at the bottom.
- Divide the meat sauce in 4 even portions and layer on top of the spaghetti squash.
- Top each container with sliced fresh mozzarella.
- Transfer containers to a pre-heated oven (350 F degrees) for 10-15 minutes. Only long enough to melt the cheese.
- Remove containers out of the oven and top with fresh basil and you are done!
