Baked Spaghetti Squash Marinara is a healthier alternative to pasta and with this super tasty marinara sauce and loads of shrimp, it is sure to be a delicious family favorite.

Gather This
With a homemade sauce and juicy shrimp, you can’t beat this spaghetti squash marinara recipe. A full list of ingredients with measurements for this recipe is available in the printable recipe card below.
- Spaghetti squash – A long, oval yellow-ish squash, it’s flesh flakes into long strands similar to pasta. Full of water and virtually flavorless, it makes the the perfect blank slate as a low carb “pasta”.
- Salt
- Pepper
- Extra virgin olive oil
- Flat anchovy fillets
- Garlic cloves
- Sweet onion
- Serrano chile
- Whole tomatoes
- Red cooking wine
- Fresh oregano leaves
- Flat leaf parsley
- Fresh basil leaves
- Sugar
- Large shrimp
- Parmesan cheese

Make it A Meal
I like to pair my spaghetti squash marinara with a nice leafy side salad and garlic bread or 2-ingredient dough breadsticks. You can also start off with a bowl of soup like pasta e fagioli or tortellini soup.
Since this dish is so full of vegetables and shrimp, it doesn’t really need a veggie side dish or additional protein.

Methods for Cooking Spaghetti Squash
You have a couple of different options for cooking the squash for spaghetti squash marinara.
- Roast in oven – Place cut side up, on a large rimmed baking sheet seasoned with sea salt and pepper. Roast at 400 degrees for 45- 60 minutes, or until it is fork tender. This is for an extra large squash. Smaller squash might only need 25-30 minutes. Check periodically for doneness. Remove from the oven and let cool for a few minutes before using a fork to pull the strands from the squash boats.
- Instant Pot – Pierce the spaghetti squash all over with a knife making sure it goes all the way through the thick walls. This helps it vent and no explode. Place it on the trivet and add 1 cup of water. Cook on manual high pressure for 15 minutes for a 3-pound squash. For a smaller squash, cook for 12 minutes and a large squash, 18 minutes.

Salt the squash before roasting to bring out moisture and then drain afterwards.
Yes, generally spaghetti squash is considered a better-for-you option than pasta. It is lower in both calories and carbs.
Spaghetti Squash Marinara with Shrimp Recipe
Equipment
Ingredients
- 2 large spaghetti squash
- coarse sea salt and ground black pepper
- 4 tablespoons extra virgin olive oil , divided
- 1 tin flat anchovy fillets
- 4-5 garlic cloves , minced
- 1 sweet onion , thinly sliced
- 1 serrano chile , minced *see note
- 28 ounce can whole tomatoes
- 1/2 cup dry red wine
- 7-8 fresh oregano sprigs
- 1/4 cup flat leaf parsley , coarsely chopped
- 1/2 cup fresh basil leaves , hand torn
- 2 tablespoons sugar
- 1 pound large shrimp , shell and tail removed, raw
- parmesan cheese , for garnish
Instructions
- Preheat the oven to 400°F. Cut the 2 large spaghetti squash in half and remove the seeds and membranes, baste with 1 tablespoon of the extra virgin olive oil on cut sides and inside.
- Place, cut side up, on a large rimmed baking sheet. Season the spaghetti squash with the coarse sea salt and ground black pepper Roast for 45- 60 minutes, or until the spaghetti squash is is fork tender. It might only take 25-30 minutes for a smaller squash. Make the sauce while the squash cooks.
- In a large skillet, heat the remaining 3 tablespoons olive oil over medium-high heat. Add the 1 tin flat anchovy fillets. They will literally melt into the olive oil. Add the minced or grated 4-5 garlic cloves, chopped 1 sweet onion and minced and seeded 1 serrano chile. Lower the heat to medium and saute until the onions are soft and opaque.
- Halve the 28 ounce can whole tomatoes, adding to mixture along with any liquid in the can and the 1/2 cup dry red wine and 7-8 fresh oregano sprigs, Simmer for 15 minutes to reduce.
- Stir in the chopped 1/4 cup flat leaf parsley, 1/2 cup fresh basil leaves, 2 tablespoons sugar and 1 pound large shrimp, Heat for 5-6 minutes or until shrimp turn pink and tails curl slightly.
- The spaghetti squash should be about done. Crispy skins should easily separate from meaty interior. Remove them from the oven.
- Set up a wire cooling rack over a rimmed baking sheet. Using a fork, rake out interior pulp of spaghetti squash. It should resemble pasta strands. Place the raked pulp onto cooling rack to allow excess liquid to drain off.
- Fork a pile of spaghetti squash onto a plate or back into the shells, followed by the shrimp marinara sauce. Garnish with freshly grated parmesan cheese , if desired.
- If you've tried this recipe, come back to let us know how it went in the comments or ratings.
Notes
Storage
Store spaghetti squash in an airtight container for up to 5 days. Reheat in the microwave or in the oven at 300°F for 10-15 minutes.Can I freeze spaghetti squash marinara?
You can freeze spaghetti squash, but keep in mind that frozen spaghetti squash may have a slightly different texture when thawed compared to fresh, as freezing can cause some moisture loss and change the texture of the strands. Chiles can have oils that will burn your finger tips. Unfortunately you won’t be able to tell if the oils are hot until you start working with the pepper. To avoid tender finger tips or *gasp* accidentally touching your eye, coat hands in olive oil, fashion plastic sandwich baggies into gloves or use powder-free latex gloves. If you do end up with sore fingers, soak them in milk or cream, the higher the fat content the better.Nutrition
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