Keto Spaghetti Casserole (Cheesy & Baked to Perfection)

If you’re anything like me, there are days when you just need a cozy, comforting dinner that doesn’t wreck your low-carb goals. That’s exactly why this baked keto spaghetti casserole has become a regular in our house. It’s hearty, cheesy, packed with flavor, and we don’t even miss the noodles.

I first made this keto spaghetti casserole on a busy weeknight when I needed something filling that my whole family would actually enjoy. That’s saying a lot since there are six of us, and several of us are picky! Between the tasty ground beef, gooey melty cheese, and tender spaghetti squash, it quickly became a favorite.

Whether you’re looking for a low-carb meal prep idea or a quick weeknight dinner, this keto baked casserole checks all the boxes. It’s simple, satisfying, and totally comforting!

Ingredients You’ll Need

This casserole keeps things simple and delicious. Here’s what I use:

• Ground beef – Hearty, filling, and flavorful. I usually go for 80/20 because the fat adds richness and keeps me fuller longer.
• Onion – Finely chopped. It adds that savory sweetness that makes the beef and sauce taste like they’ve been simmering all day.
• Low-carb spaghetti sauce – Use your favorite brand here! Look for a marinara with no added sugar. Rao’s and Classico are go-tos in our kitchen. They are rich, smooth, and packed with flavor.
• Olive oil – Just a drizzle to sauté the onions and beef. It gives everything that home-cooked taste without overpowering the dish.
• Mozzarella and Parmesan cheese – Melted, bubbly cheese on top makes this feel like comfort food at its best. I love the stretchy mozzarella and the salty kick from Parmesan. It gives the total baked spaghetti flavor.

✨ That’s it! You don’t need a long list of ingredients to make something your whole family will love.

Step-by-Step: How to Make This Keto Spaghetti Casserole

This is one of those recipes that comes together so easily yet tastes like you spent all afternoon in the kitchen.

Step 1. Preheat your oven to 375°F.

You’ll want a 9×9 baking dish lightly greased and ready to go.

Step 2. Brown the ground beef.

Add the ground beef to the skillet with the onions. Break it up with your spoon and cook until it’s browned and no longer pink. Season with a little salt and pepper if you’d like. Drain any excess grease.

Tip: I keep browned ground beef in my freezer stored in gallon freezer bags. Buying and browning ground beef in bulk is a huge meal prep hack. It makes dinners like this much easier and saves a ton of time.

Step 3. Stir in your spaghetti sauce.

Pour in the low-carb marinara and let it simmer for a couple of minutes. This gives all the flavors a chance to come together and makes your kitchen smell amazing.

Low Carb Spaghetti or Pizza Sauce Options Without Any Added Sugar

Sauce Brand	Total Carbs	Fiber	Net Carbs (½ cup)
Rao’s Homemade Marinara Sauce	6g	1g	5g
Rao’s Homemade Tomato Basil Sauce	6g	1g	5g
Lucini Italia Organic Tuscan Tomato Sauce	5g	1g	4g
Lucini Italia Organic Rustic Tomato Basil	5g	1g	4g
Victoria Trading Company Marinara Sauce	6g	1g	5g
ALDI Selected Premium Marinara	7g	2g	5g
Mezzetta Family Recipes Marinara	7g	1g	6g
Classico Tomato & Basil Pasta Sauce	8g	2g	6g

**above table is based on per serving

Step 4. Prep your spaghetti squash.

If you haven’t cooked it yet, slice your squash in half lengthwise, scoop out the seeds, coat with a thin layer of olive oil, and place it cut-side down on a baking sheet. Roast until it’s tender and shreds easily with a fork. I love to line the baking sheet with parchment paper making clean up a breeze.

Don’t skip this part—it makes a big difference!

Once your spaghetti squash is roasted and cooled a bit, place it on a few layers of paper towels and gently press out the extra moisture. You don’t want a soggy casserole, and trust me, this quick step keeps everything nice and firm when it bakes. It’s totally worth the extra minute.

Quick tip: Spaghetti squash can be a beast to cut through! To make it easier, I poke a few holes in the skin with a sharp knife and pop it in the microwave for about 3 to 5 minutes. It softens just enough to slice without a fight. If you want more help with this step, here’s a full guide on how I roast spaghetti squash that walks you through everything.

Step 5: Base layer

Place the spaghetti squash as the bottom layer in your greased 9×9 baking dish. If it seems watery at all, drain it again on paper towels before adding the sauce.

Step 6. Add the sauce.

Spoon and spread the meat sauce on top of the shredded squash base.

Step 7. Top with cheeses.

Add the mozzarella, parmesan cheese, and Italian seasoning to the keto spaghetti casserole.

Step 8. Bake until bubbly.

Pop the casserole into the oven and bake uncovered until the cheese is melted and starting to turn golden brown around the edges. If you like the cheese a little crispy on top, you can broil it for the last 1–2 minutes. Just keep a close eye on it.

How to Store & Reheat Leftovers

This keto spaghetti casserole stores really well. Honestly, I think the flavors get even better the next day. Here’s how I handle leftovers (when we actually have any!):

Refrigerator:

Let the casserole cool completely, then cover the baking dish with foil or put leftovers in an airtight container. It’ll keep in the fridge for 3–4 days.

Freezer:

This recipe freezes great! Wrap it in foil and place in a zippered storage bag or use a freezer-safe container, and store for up to 2–3 months.

Reheating:

To reheat from the fridge, pop it in the microwave for about 60–90 seconds. For the best texture, especially if it was frozen, I recommend reheating it in the oven at 350°F for about 15–20 minutes or until warm.

Pro tip: Add a tiny splash of marinara on top before warming it up.

Recipe Variations & Easy Substitutions

This casserole is super flexible so don’t stress if you want to tweak it. Here are a few ways it can be switched up:

Use ground turkey or sausage instead of beef

Ground turkey is a great lighter option that works great. Want more flavor? Try Italian sausage (just watch the carbs—some brands can sneak in sugar).

Make it dairy-free

You can skip the cheese entirely or swap in a dairy-free mozzarella-style blend.

Add in veggies

Chopped spinach, zucchini, or mushrooms are fantastic additions. It’s an easy way to sneak in extra nutrients especially if you’re feeding kids.

Want it spicy?

A pinch of red pepper flakes or a little hot Italian sausage brings the heat. My husband’s a fan, but I usually keep it mild for the kids.

Use hearts of palm noodles.

If you want more of a traditional “pasta bake” texture, then try subbing some or all of the spaghetti squash for palmini noodles. They’re low in carbs and surprisingly close to the real thing!

What do I serve with it?

• Keto Cheesy Garlic Chaffle Bread
• Keto Cheesy Breadsticks
• Steamed Broccoli
• Fresh Leafy Garden Salad

If you’re looking for a cozy, satisfying meal that doesn’t feel like “diet food,” this baked keto spaghetti casserole is it. It’s cheesy, hearty, and full of flavor.

Whether you’re just starting out on a low-carb journey or you’ve been eating this way for years, I hope this becomes one of those go-to dinners you come back to again and again.

If you try it, I’d love to hear what you think! Drop a comment below, leave a ⭐⭐⭐⭐⭐ rating, or tag me on Instagram so I can see your version!

** And don’t forget to save or pin this recipe so you’ve got it ready the next time you need an easy, family-friendly keto dinner. **

More Easy Keto Casserole Recipes

• Easy Spaghetti Sauce Lasagna Boats
• The BEST Easy Keto Baked Italian Sausage
• Keto Italian Meatball Casserole