Spaghetti Squash Au Gratin Casserole (Baked Cups Option)

Make Spaghetti Squash Au Gratin in a casserole dish or muffin pan. This cheesy, low‑carb side is a crowd pleaser—perfect for Thanksgiving, fall dinners, or any time you want a lighter alternative to starchy sides. Turn it into individual muffin‑style cups to entice kids and guests with single‑serve portions.

This easy spaghetti squash casserole is rich and creamy with a golden, cheesy top—true to the meaning of “au gratin.” It’s gluten‑free and keto‑friendly when you skip higher‑carb add‑ins, and it reheats well for make‑ahead meals or holiday planning.

Ingredients

Gather the following for a creamy, cheesy au gratin that serves about 6 (or makes 18 muffin‑sized cups):

• 4 cups spaghetti squash strands (cooked; about 1 medium squash)
• 1 teaspoon olive oil
• 1 cup diced onion (about 1 small onion)
• 1/2 cup sour cream (or plain Greek yogurt)
• 2 eggs, lightly beaten
• 1 cup shredded cheddar cheese, divided
• 1/2 teaspoon garlic powder
• 1/4 teaspoon salt, or to taste

The recipe card below includes ingredient amounts, step‑by‑step instructions, and nutrition information.

How to Make Spaghetti Squash Strands

The key step is cooking the squash. You’ll need about 4 cups of cooked strands. One medium squash usually yields the right amount. You can prepare the strands a few days ahead and refrigerate them until ready to assemble.

Prep the Gourd (Any Method)

Poke the squash with a sharp knife tip about 1/2 inch deep in at least 10 places to let steam escape. If you prefer to halve the squash before roasting, microwave the whole punctured squash for 1–2 minutes to soften the skin for easier cutting.

Cook Whole Squash (Oven or Slow Cooker)

To cook whole:

1. Place the prepped squash in a slow cooker (covered) or on a baking sheet in a 425°F oven.
2. Slow cooker: cook on low 5–6 hours or high 3–4 hours, until a knife inserts easily. Oven: roast about 30 minutes, turning once.
3. Cool 10 minutes, cut in half, remove seeds, and use a fork to scrape out the strands.

Cook Halves in the Oven

For the halved method:

1. Cut squash in half and remove seeds.
2. Brush flesh with olive oil and season with salt and pepper.
3. Place flesh‑side down on a foil‑lined sheet pan.
4. Bake at 375°F for about 40 minutes, until tender. Scrape strands with a fork.

Directions with Pictures

Once your squash strands are ready, follow these steps to make either a casserole or muffin‑style cups.

1. Preheat oven to 350°F.
2. Heat olive oil in a skillet over medium. Sauté diced onion about 5 minutes, until tender.
3. In a large bowl combine drained spaghetti squash strands, sautéed onion, sour cream (or yogurt), garlic powder, salt, eggs, and 1/2 cup of the shredded cheddar. Mix gently to combine. Drain any excess liquid from the strands first, but you don’t need to squeeze them dry.
4. Spread mixture into a buttered 8 x 10 casserole dish, or portion into a standard muffin pan sprayed with nonstick spray (makes about 18 cups).
5. Sprinkle remaining cheddar cheese evenly over the top.
6. Bake about 25 minutes until set and starting to brown. Switch the oven to broil and broil 2–3 minutes to crisp and color the tops—watch closely to prevent burning.
7. Let cool 5–10 minutes before serving so portions hold their shape.

Muffin Pan Method

Use the same mixture and divide into a greased or sprayed muffin pan. Allow at least 10 minutes to set before carefully removing each cup with a nylon spatula. These individual portions are great for parties and kid‑friendly servings.

Storage and Make Ahead Tips

Refrigerator: Store leftovers in an airtight container up to 3 days.

Make Ahead:

• Cook and refrigerate spaghetti squash strands up to 5 days before assembling.
• Prepare the casserole or cups the day before and bake the next day.
• Fully cook, then reheat the next day in a 350°F oven.

Freezer: This recipe freezes well before or after baking. To freeze uncooked, assemble in a freezer‑safe dish, cover tightly, and freeze up to 2 months. Defrost overnight in the refrigerator and bake as directed. If reheating a previously cooked, frozen casserole, warm in a 350°F oven until an internal temperature of 145°F is reached; tent with foil if browning too quickly. Microwaving is not recommended for best texture.

Variations

Customize the dish to suit your taste or turn it into a main course:

• Caramelize the onions for deeper flavor.
• Add red pepper flakes or a pinch of cayenne for heat.
• Stir in up to 1 cup diced or shredded cooked chicken to make it a main dish.
• Add up to 1 cup crumbled cooked bacon for a smoky twist.
• Return the mixed filling to the hollowed squash halves and bake as spaghetti squash “boats.”

More Spaghetti Squash Recipes

📋 Recipe