Give your comfort food a low-carb glow-up with this easy, cheesy, vegetarian-friendly casserole!

Casseroles make such easy meals. You do a little prep, pour everything into a dish, then let the oven do all the work while you tidy up. This squash casserole recipe has become a favorite because it checks all the dietary boxes for my family. It’s meatless, so my vegetarian sister will eat it. It’s low in carbs, so my partner and I can enjoy it with her. Plus, it’s ridiculously cheesy and delicious, so my picky nieces and nephews like it, too!
This dish comes together quickly, as well, with only about 10 minutes of hands-on work before baking it. And the flavors make it a comfort-food dream! Each bite delivers a satisfying medley of earthy squash, savory onions and garlic, and slightly sweet oregano and thyme—all robed in a rich, creamy cheese sauce.
I make this dish on weeknights when summer starts to fade into an autumn chill. It’s a great way to use up the squash overflow from my friends’ gardens near the end of harvest time. And it warms our hearts as it fills our bellies with veggie goodness.

Tips for a spectacular squash casserole
First, I recommend using a mandoline to get evenly sliced squash. When the slices are uniform, they cook more consistently. Then I suggest you sprinkle your squash slices with a little salt and let them sit in a strainer for about 15 minutes before adding them to the other ingredients. This will draw out a lot of their excess moisture, which will help keep your casserole from getting soggy.
This recipe calls for fresh onion and garlic—and I strongy advise against subbing in their powdered forms! Fresh ingredients imbue your casserole with more vibrant flavors, and it only takes a few moments to prepare them.
An ingredient you can switch up is the cheese. While I love the sharp, tangy combo of cheddar and Parmesan in this recipe, you could opt for other pairings. Mozzarella has a mild flavor and melty texture that goes very well with the salty punch of pecorino Romano. The bold, nutty notes of Gruyère make a lovely counterpoint to the gentle creaminess of fontina. And if you’re looking for a cheese combo that’s lower in lactose but big on tangy, briny flavors, consider goat cheese and feta.
Finally, if you want an eye-catching golden brown top on your casserole, put it under the broiler for the final two or three minutes of baking. Watch it closely, though, so it doesn’t burn!

How do I store leftovers?
Let the casserole cool to room temp before storage, but don’t let it sit out for longer than 2 hours. Store leftovers in an airtight container in the fridge for up to 4 days or in the freezer for up to 4 months. Thaw overnight in the fridge. Reheat individual portions in the microwave in short intervals, stirring in between to ensure even heating. Larger amounts reheat more evenly in the oven at 325°F, covered, for about 10-15 minutes.

Similar recipes to try
Looking for other hearty, veggie-forward casseroles to try? Check out this Low-Carb Broccoli Cheese Casserole, this Keto Green Bean Casserole, and this Delicious Low-Carb Cauliflower Casserole. Want a less-cheesy way to enjoy squash? Try this recipe for Maple Spice Roasted Acorn Squash that’s low-carb and paleo-friendly.


Squash Casserole Recipe
Ingredients
- 3 tablespoons unsalted butter
- 1 small onion finely diced
- 2 cloves garlic minced
- 2 pounds zucchini and yellow summer squash sliced into thin rounds
- 1/2 teaspoon dried thyme
- 1/2 teaspoon dried oregano
- 1/2 teaspoon salt
- 1/4 teaspoon black pepper
- 1 cup sour cream
- 2 large eggs
- 2 cups cheddar cheese grated and divided
- 1/2 cup Parmesan cheese grated
Instructions
- Preheat your oven to 350°F. Prepare a casserole dish with nonstick spray and set it aside.

- In a large skillet, melt the butter over medium heat. Add the diced onion and minced garlic. Sauté until the onions become translucent and the garlic becomes fragrant, about 2-3 minutes.

- Add the sliced squash to the skillet. Cook until they soften slightly, about 5 minutes. Stir in the thyme, oregano, salt, and black pepper. Remove from heat.

- In a separate mixing bowl, whisk together the sour cream and eggs until well combined. Stir in one cup of the cheddar cheese. Add the squash and onions to the egg mixture. Stir until the veggies are coated completely.

- Pour the entire mixture into the prepared casserole dish.

- Sprinkle the Parmesan cheese and remaining cheddar over the top of the squash mixture and pop the dish into the oven. Bake until the casserole is bubbly and the cheese is beautifully golden brown on top, about 20-30 minutes.

- Remove the casserole from the oven and let it rest for 10-15 minutes before slicing. Serve warm.


Hi,
I want to make this but I noticed it is only using 1 cup of the cheddar and you talk about mozzarella and that is not listed as an ingredient. Would you please clarify? thanks
Hi, this is a typo, it should read cheddar instead of mozzarella. Thanks for flagging!