Transform your side dish game with this incredibly delicious and easy-to-make Spaghetti Squash Au Gratin! Whether baked in a classic casserole dish or charming individual muffin cups, this cheesy, low-carb delight is guaranteed to be a sensational hit at any meal. It’s the perfect healthy alternative to traditional starchier sides, making it a favorite for Thanksgiving dinner, fall gatherings, or any weeknight feast. Keto-friendly and gluten-free, this recipe ensures everyone can enjoy a flavorful and satisfying vegetable dish.

This simple yet elegant recipe takes wholesome spaghetti squash and elevates it into a rich, savory casserole. It’s an ideal way to sneak more vegetables onto the plate, especially for those picky eaters! When presented as mini casserole cups, even children get excited about their greens, as who can resist their very own single-serving “muffin”? We’ve seen this magic work wonders with our Cauliflower Cheese Muffins and Broccoli Muffins, and it’s no different here!
The term “au gratin” isn’t just a fancy culinary phrase; it promises a glorious golden, bubbly cheese crust that crowns each serving, delivering an irresistible texture and flavor. So, whether you choose the full casserole or the adorable spaghetti squash cups, you’re signing up for a truly cheesy, comforting dream that will impress family and friends alike. Prepare to enjoy a low-carb side dish that truly shines!

Why Spaghetti Squash Au Gratin is a Must-Try
If you’re looking for a delightful and healthy addition to your meal rotation, Spaghetti Squash Au Gratin is an excellent choice. This dish offers a fantastic combination of health benefits and incredible flavor, making it a win-win for any home cook. Spaghetti squash itself is a nutritional powerhouse, low in calories and carbohydrates, yet rich in vitamins, minerals, and dietary fiber. It’s a superb natural pasta alternative for those following a keto, gluten-free, or low-carb diet, helping you maintain your dietary goals without sacrificing taste.
The “au gratin” preparation transforms the mild flavor and spaghetti-like texture of the squash into something truly decadent. By baking it with a creamy, cheesy sauce and a golden crust, you create a comforting dish that feels indulgent but remains remarkably light and nutritious. It’s versatile enough to be a festive holiday side, a cozy weeknight staple, or even a light main course when augmented with protein. Plus, the visually appealing presentation, especially in individual cups, adds a touch of elegance and fun to your dining experience.
Ingredients for Your Cheesy Spaghetti Squash Au Gratin
Creating this savory spaghetti squash au gratin requires a handful of simple, wholesome ingredients that come together to form a rich and satisfying dish. Here’s what you’ll need to gather:

- Spaghetti Squash Strands: The star of our dish! You’ll need about 4 cups of cooked spaghetti squash strands, typically from one medium-sized squash. Its unique texture mimics pasta, making it an excellent low-carb base. (Refer to the next section for various easy cooking methods.)
- Sour Cream: This adds a wonderful creamy texture and tangy depth to the casserole. For a protein boost and slightly lighter option, feel free to substitute with plain Greek yogurt.
- Eggs: Essential for binding all the ingredients together, ensuring your au gratin holds its shape beautifully whether baked in a dish or individual cups. Lightly beaten eggs integrate smoothly into the mixture.
- Onion: Finely diced and sautéed until tender, onion provides a foundational aromatic flavor that complements the squash and cheese perfectly.
- Cheddar Cheese: Sharp cheddar is recommended here for its robust flavor, which contrasts beautifully with the mildness of spaghetti squash. Half will be mixed into the casserole, and the other half generously sprinkled on top for that iconic golden, bubbly crust.
- Garlic Powder: Offers a subtle, savory garlic note without overwhelming the other flavors. It’s a convenient way to add depth to the dish.
- Olive Oil: Used for sautéing the diced onions, olive oil adds a touch of healthy fat and helps to develop their sweetness.
- Salt and Pepper: Fundamental seasonings to enhance and balance all the flavors. Adjust to your personal taste.
For exact measurements and detailed instructions, please refer to the comprehensive recipe card provided further down in the article.
How to Prepare Perfect Spaghetti Squash Strands
The most crucial step in making any spaghetti squash recipe, including this delicious au gratin, is properly cooking the squash to yield those desirable, pasta-like strands. The good news is there are several straightforward methods, and you can even prepare the squash several days in advance to streamline your cooking process. For this recipe, you’ll need approximately 4 cups of cooked spaghetti squash strands, which typically comes from one medium-sized squash.
Prepping the Gourd (for all methods)
Regardless of your chosen cooking method, a little initial preparation goes a long way. First, carefully stab the outside of the spaghetti squash with the tip of a sharp knife. Make at least 10 cuts, or more for larger gourds, to allow steam to escape during cooking. This prevents the squash from exploding and helps it cook more evenly.
If you plan to cut the spaghetti squash in half *before* cooking (as in the traditional oven method), a quick microwave trick can make this task much safer and easier. After poking holes, place the squash on a microwave-safe plate and cook on high for 1-2 minutes. This brief softening makes cutting through the tough skin significantly simpler and reduces the risk of injury.
Cooking Whole Spaghetti Squash (Oven or Slow Cooker)
Cooking spaghetti squash whole is an incredibly simple, hands-off method that minimizes effort and mess. Once cooked, slicing it open and extracting the strands becomes a breeze.
- Place your prepped (and poked) spaghetti squash in either a slow cooker or on a baking sheet in an oven preheated to 425°F (220°C).
- Slow Cooker Method: Cover the slow cooker and cook on low for 5-6 hours, or on high for 3-4 hours. The squash is ready when a knife can be easily inserted into its skin with minimal resistance. This method is great for tender, moist squash.
- Oven Roasting (Whole): Roast the squash for about 30 minutes, rolling it over halfway through to ensure even cooking. This high-heat method can yield a slightly drier, more defined strand texture.
- After cooking, allow the spaghetti squash to cool for about 10 minutes. This makes it much safer and easier to handle. Carefully cut the squash in half lengthwise and scoop out the seeds. Then, use a fork to gently scrape the spaghetti-like strands from the insides of the squash halves.
Cooking Spaghetti Squash Halves in the Oven (Traditional Method)
This is arguably the most common and traditional way to prepare spaghetti squash, offering excellent flavor and texture.
- Using a sharp knife and a steady surface (or after softening in the microwave as described above), carefully cut the spaghetti squash in half lengthwise. Scoop out and discard the seeds and fibrous membranes.
- Lightly brush the cut surfaces of the squash halves with olive oil and season generously with salt and black pepper. This helps to enhance the flavor and promote browning.
- Place the seasoned squash halves, flesh side down, onto a baking sheet lined with aluminum foil or parchment paper for easy cleanup.
- Bake in a preheated 375°F (190°C) oven for approximately 40 minutes, or until the flesh is tender when poked with a fork. The exact time may vary depending on the size of your squash.
- Once tender, remove from the oven and allow to cool slightly. Use a fork to scrape the delicious spaghetti-like strands from the squash shells.

No matter which method you choose, always ensure the squash is adequately drained of excess liquid after cooking. While this recipe doesn’t require extreme squeezing, a quick drain will prevent a watery casserole and ensure your au gratin has the perfect creamy consistency.
Step-by-Step Directions for Assembling Your Au Gratin
Once you have your perfectly cooked spaghetti squash strands ready, assembling this au gratin is a straightforward and rewarding process. We’ll guide you through making both a classic casserole in an 8x
