Baked Spaghetti Squash Casserole

This healthy Baked Spaghetti Squash Casserole is loaded with tender spaghetti squash, a hearty homemade meat sauce and plenty of melty cheese. It’s a cozy, satisfying, low-carb dinner the whole family will love!

There’s nothing better than a warm, cheesy casserole for an easy family dinner, and this Baked Spaghetti Squash Casserole is one of our favorites! It has all the comforting Italian flavors of baked pasta, but roasted spaghetti squash takes the place of traditional noodles.

The spaghetti squash is layered with a rich homemade meat sauce, fresh basil, Parmesan and gooey mozzarella, then baked until hot and bubbly. It’s hearty, packed with vegetables and makes plenty of leftovers for lunch the next day.

The key to keeping spaghetti squash casserole from becoming watery is roasting the squash until it is just tender, draining the strands well and allowing the meat sauce to simmer until thick. These simple steps give you a perfectly saucy casserole without excess liquid collecting in the bottom of the baking dish.

Why You’ll Love This

• Healthy and satisfying – spaghetti squash makes a delicious low-carb and gluten-free alternative to traditional pasta.
• Protein-packed – lean ground beef makes this casserole filling enough to serve as a complete meal.
• Full of flavor – a rich tomato meat sauce, Italian seasoning, fresh basil and two kinds of cheese give it classic Italian flavor.
• Great for meal prep – prepare the components ahead of time and assemble the casserole when you’re ready to bake.
• Perfect for leftovers – the flavors are even better the next day!

Ingredients You’ll Need

• spaghetti squash – use one medium-large spaghetti squash that yields approximately 6 cups of cooked strands. Measuring the cooked squash prevents the casserole from becoming watery or overloaded with squash.
• olive oil – used for roasting the squash and sautéing the onion and garlic.
• onion and garlic – create a flavorful base for the homemade meat sauce.
• lean ground beef – I used 95% lean ground beef, but ground turkey or ground chicken would also work.
• crushed tomatoes – form the base of the tomato sauce.
• tomato sauce + tomato paste – adds rich tomato flavor while helping to thicken the meat sauce so the casserole doesn’t turn out too watery.
• Italian seasoning – a convenient blend of herbs that pairs perfectly with the tomatoes and beef.
• honey – optional, but a small amount balances the acidity of the tomatoes.
• Parmesan cheese – adds savory, salty flavor to both the sauce and the top of the casserole.
• fresh basil – adds fresh Italian flavor. Save some for sprinkling over the finished casserole.
• mozzarella cheese – melts over the casserole for the perfect cheesy topping.
• salt and pepper – enhances all the flavors.

How to Make Baked Spaghetti Squash Casserole

1. Roast the squash. Cut the spaghetti squash in half, remove the seeds and brush with olive oil. Season with salt and pepper, then roast cut-side down at 400°F for 35 to 40 minutes, until just tender.
2. Make the meat sauce. Sauté the onion and garlic, then add the ground beef and cook until browned. Stir in the tomato paste, crushed tomatoes, tomato sauce, seasonings and honey. Simmer uncovered for 15 to 20 minutes, until thickened, then stir in the Parmesan and fresh basil.
3. Drain the squash. Scrape the cooked squash into strands and let them drain in a colander for 5 to 10 minutes. Gently blot away any excess moisture to prevent a watery casserole.
4. Assemble the casserole. Toss the drained spaghetti squash with the meat sauce, then spread the mixture into a greased 9×13-inch baking dish. Sprinkle the mozzarella evenly over the top.
5. Bake and serve. Bake uncovered at 375°F for 20 to 25 minutes, until hot and bubbly. Let the casserole rest for 10 minutes before serving, then garnish with fresh basil.

Tips for the Best Spaghetti Squash Casserole

• Measure the cooked squash. Spaghetti squash can vary greatly in size. For the best ratio of squash to meat sauce, use approximately 6 cups of cooked strands.
• Don’t overcook the squash. Roast it only until the strands are just tender. Mushy, overcooked squash releases substantially more water.
• Drain it well. Let the cooked strands sit in a colander for at least 10 minutes and gently press out excess moisture.
• Thicken the sauce. Simmer the meat sauce uncovered until it is thick rather than runny. Dragging a spoon through the skillet should briefly leave a visible path.
• Bake the casserole uncovered. Covering it with foil traps steam and can make the finished casserole watery.
• Let it rest. Allow the casserole to sit for 10 to 15 minutes before serving so it holds together better.
• Use freshly shredded cheese. It melts more smoothly than packaged pre-shredded cheese.

Variations and Substitutions

• Ground turkey or chicken – Swap the ground beef for lean ground turkey or ground chicken.
• Italian sausage – Use mild or spicy Italian sausage for even more flavor.
• Vegetarian – Leave out the meat and add sautéed mushrooms, zucchini, bell peppers or chopped spinach.
• Add more vegetables – Sauté mushrooms, spinach or bell peppers with the onion. Make sure to cook off any liquid before adding them to the sauce.
• Make it spicy – Add crushed red pepper flakes to the meat sauce.
• Different cheese – Try provolone, fontina or an Italian cheese blend in place of some of the mozzarella.

What to Serve with Spaghetti Squash Casserole

This casserole is hearty enough to enjoy on its own, but you can also serve it with a simple green salad or roasted vegetables. My garlic parmesan Brussels sprouts would be delicious alongside this casserole, or pair it with perfectly roasted broccoli and sweet potatoes for even more vegetables.

If you want something to soak up the extra meat sauce, serve it with warm honey cornbread mini muffins or your favorite garlic bread.

Prepping Ahead of Time

You can roast and drain the spaghetti squash and prepare the meat sauce up to 2 days in advance. Store them separately in airtight containers in the refrigerator, then assemble and bake the casserole when you’re ready to eat.

You can also assemble the entire casserole one day ahead. Make sure both the squash and sauce have cooled completely before layering everything in the baking dish. Cover and refrigerate without baking. When ready to cook, uncover the casserole and let it sit at room temperature while the oven preheats. Add approximately 5 to 10 minutes to the baking time if it is still cold from the refrigerator.

Frequently Asked Questions