This Spaghetti Squash Au Gratin is a lighter, vegetable-forward take on the classic comfort food side dish. By swapping potatoes or pasta for tender strands of spaghetti squash, you get a satisfying meal that is lower in carbs but still packed with savory, cheesy flavor.
With a creamy, seasoned filling and a golden brown Cheddar crust, this gratin is the perfect guilt-free indulgence for any night of the week.
Recipe Details
- Flavor Profile: This dish features the mild sweetness of squash enhanced by caramelized onions and savory garlic powder, with a gentle kick of heat from red pepper flakes.
- Texture: The spaghetti squash provides tender, pasta-like strands that hold up well against the creamy sour cream binder and the melted cheese topping.
- Time: 15 minutes prep/microwave, 25 minutes bake time.
- Difficulty: Easy. The microwave method for the squash makes the prep work incredibly fast.
What You’ll Need
To make this recipe, you will need a microwave-safe dish to steam the squash quickly. You will also need a medium skillet to sauté the aromatic onion mixture and a baking dish for the final assembly. The ingredients utilize lighter dairy options like fat-free sour cream and light Cheddar cheese to keep the dish wholesome without sacrificing creaminess.
Ingredient Notes
- Spaghetti Squash – You need one squash, halved and seeded. When cooked, the flesh scrapes out into long strands resembling spaghetti.
- Light Margarine – Used to sauté the onions, adding a buttery flavor while keeping the fat content lower.
- Yellow Onion – Thinly slicing the onion and browning it adds a deep, savory flavor that contrasts nicely with the creamy sauce.
- Red Pepper Flakes – A teaspoon gives this dish a surprising and delightful amount of heat. You can adjust this if you prefer a milder taste.
- Fat-Free Sour Cream – This acts as the creamy binder for the casserole, adding tang and richness without the heaviness of heavy cream.
- Light Cheddar Cheese – Divided into the mixture and on top, this provides the essential cheesy pull and golden crust.
Add-ins and Substitutions
- Herbs – Fresh chopped parsley or chives sprinkled on top after baking adds a nice pop of color and freshness.
- Garlic – If you love garlic, you can add a clove of fresh minced garlic to the skillet along with the garlic powder.
- Vegetables – You could stir in steamed broccoli florets or spinach into the squash mixture before baking for extra greens.

How to Make Spaghetti Squash Au Gratin
- Cook the Squash: Place the halved and seeded spaghetti squash in a microwave-safe covered dish and add 1/4 inch of water. Microwave for 10 to 12 minutes. Once cool enough to handle, scrape the insides of the squash with a fork to create strands and transfer them to a small bowl.
- Sauté Aromatics: While the spaghetti squash is cooking, heat the light margarine in a medium skillet over medium heat. Cook the thinly sliced onion, red pepper flakes, garlic powder, salt, and freshly ground black pepper until the onion is browned, which should take about 5 to 10 minutes.
- Prep the Oven: Preheat the oven to 375 degrees F (190 degrees C). Grease a baking dish with nonstick cooking spray.
- Combine: Mix the cooked spaghetti squash strands, the browned onion mixture, fat-free sour cream, and 1/2 of the shredded light Cheddar cheese together until well combined.
- Assemble: Transfer the mixture to the prepared baking dish and smooth it out. Top evenly with the remaining Cheddar cheese.
- Bake and Broil: Bake in the preheated oven for 20 to 25 minutes until heated through. Turn on the broiler for the last 2 to 3 minutes and broil until the gratin is golden brown on top.
Pro Tip: Be careful when removing the squash from the microwave. The steam trapped inside the covered dish will be extremely hot. Lift the lid away from your face to let the steam escape safely.
Recipe Tips
- Browning Onions: Don’t rush the onions. Letting them get truly browned and caramelized in the margarine adds a depth of flavor that makes this dish taste rich.
- Broiler Watch: When you switch the oven to broil for the final few minutes, keep a close eye on the cheese. It can go from golden brown to burnt in seconds.
- Fork Technique: When scraping the squash, use a large fork and scrape horizontally across the squash to get the longest “noodle” strands possible.

FAQs
- Is this dish spicy? With a full teaspoon of red pepper flakes, it has a definite kick. If you are sensitive to spice, you may want to reduce it to 1/4 or 1/2 teaspoon.
- Can I prepare the squash ahead of time? Yes, you can microwave and scrape the squash a day in advance. Store the strands in the fridge until you are ready to make the filling and bake.
- How do I store leftovers? Store any leftovers in an airtight container in the refrigerator for up to 3 days. Reheat in the microwave or oven until warm.
Serving Suggestions
- Roasted Chicken: This cheesy side dish pairs perfectly with a simple roast chicken or turkey breast.
- Steak: Serve alongside a grilled steak for a lower-carb alternative to potatoes au gratin.
- Green Salad: A crisp green salad with a vinaigrette dressing cuts through the richness of the cheese and sour cream.
Make This Recipe in Advance
- Prep: You can cook the squash and sauté the onions in advance. Store them separately in the fridge.
- Assembly: You can mix the entire casserole, put it in the baking dish, and cover it. Store in the fridge for up to 24 hours before baking. You may need to add a few minutes to the baking time if starting with a cold dish.
Spaghetti Squash Au Gratin
- Total Time: 40 minutes
- Yield: 4 Servings 1x
- Diet: Vegetarian
Description
This Spaghetti Squash Au Gratin is the perfect way to enjoy a creamy, cheesy comfort food side dish without the carb-heavy guilt. By swapping pasta or potatoes for tender spaghetti squash strands, this recipe creates a vegetable-forward casserole featuring sweet caramelized onions, a kick of red pepper flakes, and a golden, bubbly light Cheddar crust. It is a wholesome, savory indulgence suitable for any weeknight meal.
Ingredients
- 1 spaghetti squash, halved lengthwise and seeded
- 3 tablespoons light margarine
- 1 small yellow onion, thinly sliced
- 1 teaspoon red pepper flakes
- 1/4 teaspoon garlic powder
- Salt and freshly ground black pepper to taste
- 3/4 cup fat-free sour cream
- 1 cup shredded light Cheddar cheese, divided
- Cooking spray
Instructions
Cook the Squash
Place the halved and seeded spaghetti squash in a microwave-safe dish with a lid. Add about 1/4 inch of water to the dish. Cover and microwave on high for 10 to 12 minutes. Once it is cool enough to handle, use a fork to scrape the flesh horizontally to create long strands. Transfer the strands to a bowl.
Sauté the Aromatics
While the squash is cooking, melt the light margarine in a medium skillet over medium heat. Add the thinly sliced onion, red pepper flakes, garlic powder, salt, and black pepper. Sauté until the onions are thoroughly browned and caramelized, about 5 to 10 minutes.
Prep the Oven
Preheat your oven to 375°F (190°C). Grease a baking dish with nonstick cooking spray.
Combine the Mixture
In a bowl, mix the cooked spaghetti squash strands, the browned onion mixture, the fat-free sour cream, and 1/2 cup of the shredded light Cheddar cheese. Stir until well combined.
Assemble the Gratin
Transfer the squash mixture to the prepared baking dish and smooth the top. Sprinkle the remaining 1/2 cup of Cheddar cheese evenly over the casserole.
Bake and Broil
Bake in the preheated oven for 20 to 25 minutes until heated through. For a crispy crust, switch the oven to broil for the last 2 to 3 minutes, watching carefully until the cheese is golden brown.
Notes
Spice Level: This recipe uses 1 teaspoon of red pepper flakes for a noticeable kick. If you prefer a milder flavor, reduce this to 1/4 teaspoon or omit it entirely.
Safety Tip: Be extremely careful when removing the lid from the microwave dish after cooking the squash; steam will escape rapidly. Lift the lid away from your face.
Make Ahead: You can cook the squash and sauté the onions a day in advance. Store them in the fridge, then mix and bake when ready to serve.
- Prep Time: 15 minutes
- Cook Time: 25 minutes
- Category: Side Dish
- Method: Baking
- Cuisine: American
Nutrition
- Serving Size: 1 Serving
- Calories: 195
- Sugar: 8g
- Sodium: 480mg
- Fat: 9g
- Saturated Fat: 4g
- Unsaturated Fat: 3g
- Trans Fat: 0g
- Carbohydrates: 18g
- Fiber: 3g
- Protein: 12g
- Cholesterol: 25mg
Keywords: spaghetti squash au gratin, low carb side dish, vegetarian casserole, healthy comfort food, cheesy squash recipe, keto friendly sides, vegetable gratin


