Creamy Butternut Squash Gratin with Caramelized Onions

Name: Creamy Butternut Squash Gratin
Prep time: 20 min
Cook time: 60 min
Total time: 85 min
Ingredients: 1 butternut squash (about 2 pounds); 4 tablespoons butter; 1 large onion sliced; 4 garlic cloves; 12 sage leaves (cut into thin strips); 1 tablespoon fresh thyme leaves; 1 teaspoon sea salt; ½ teaspoon black pepper; ⅛ teaspoon nutmeg; 1 cup heavy cream; ½ cup grated Parmesan cheese; ¼ cup breadcrumbs

Modified: Oct 30, 2025 · Published: Nov 15, 2016 by Anya · This post may contain affiliate links · 31 Comments

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This scalloped butternut squash gratin is made with caramelized onions, sage, garlic, and thyme in a creamy sauce, layered and topped with Parmesan cheese and breadcrumbs, then baked until golden and bubbling.

butternut squash gratin in baking dish with a serving spoon.

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💡Recipe Overview
Ingredients for Butternut Squash Gratin
How to Make Butternut Squash Gratin
Helpful Tips
Serving Suggestions
Frequently Asked Questions
Printable Recipe

💡Recipe Overview

Prep and Cook Time: 20 minutes to prep and 1 hour to bake
Cooking Method: Stove-top for cream sauce, then oven-baked
Dietary Info: Primal, GAPS, Ancestral diet
Tools Needed: Casserole dish
Skill Level: Moderate

What is an ancestral diet? Read my post on what nourishing foods are based on the traditional dietary principles of the Weston A. Price Foundation.

Reasons to Love this Butternut Squash Gratin

I used to think butternut squash was just ...fine. Nothing to get excited about. Then I tried this gratin, and I've been hooked ever since.

Tender, naturally sweet squash gets cozy with savory, creamy sauce that's basically begging to be devoured. It's the perfect mix of sweet and savory, rich but not heavy, and just plain delicious. And that pinch of nutmeg - chef's kiss!

Serve it alongside roast chicken, spatchcock turkey, or slow cooker duck - either way, it disappears fast.

One bite and you'll be rethinking everything you thought you knew about squash.

Ingredients for Butternut Squash Gratin

Butternut squash – choose a firm, heavy squash with smooth skin. Peel, seed, and slice thinly (about ⅛ inch thick) for tender, evenly cooked layers.
Onion – caramelized onion adds natural sweetness and rich flavor depth.
Garlic – freshly minced garlic gives a savory, aromatic boost.
Butter – adds richness and helps caramelize the onions for a deeper, buttery flavor.
Fresh herbs – sage and thyme bring a warm, earthy flavor that pairs beautifully with squash. You can use dried but fresh herbs are abundant this time of year and it truly does make a difference in this gratin.
Heavy cream – makes a smooth, velvety sauce that binds the layers together.
Parmesan cheese – adds a salty, nutty flavor and helps form a golden, crisp topping.
Breadcrumbs – provide a light crunch on top; use gluten-free or omit if preferred.
Seasoning blend – a balanced mix of sea salt, black pepper, and a pinch of nutmeg enhances the cream sauce and highlights the sweetness of the squash.

graphic of fork and spoon connected in a plant.

Make it Ancestral

Use quality ingredients like fresh, locally grown butternut squash, grass-fed butter, and raw cream if accessible. Choose aged Parmesan for better digestibility and deeper flavor.

butternut squash gratin slice on a plate with a fork infront of baking dish.

How to Make Butternut Squash Gratin

The complete printable recipe is below in the recipe card for your convenience. Follow these simple step-by-step instructions for the best results.

Step 1. Slice

Peel butternut squash and cut lengthwise. Remove seeds and pith. Thinly slice crosswise into ⅛-inch thick circles. You can also cut into half-moons.

Step 2. Saute

Melt butter in a large skillet over medium heat. Add sliced onions and season with salt to release juices. Cook until onions are caramelized (approximately 25 minutes), stirring occasionally.

carmalized onions cooking in pan with added ingredients.

Step 3. Add

Add garlic, sage leaves, thyme, and season with salt, pepper, and nutmeg and cook just until fragrant.

creamy carmalized onion sauce cooking in a pan.

Step 4. Simmer

Reduce heat to medium-low and add heavy cream. Whisk to combine everything and cook until cream sauce has thickened.

Step 5. Layer

Spoon ¼ of the onion cream mixture to the bottom of the casserole dish. Arrange odds and ends of butternut squash slices across the dish, overlapping slightly. Spoon another ¼ of the cream onion mixture. Add a second layer of the butternut squash, followed by the 3rd ¼ of the onion cream mixture.

carmalized onion sauce covering the squash slices with bread crumbs on top, in a baking dish.

Step 6. Bake

Add the final layer of butternut squash, overlapping and pressing down so the top is flat all across the baking dish. Drizzle the remaining onion mixture. Spread the cream onion sauce evenly to cover the squash. Sprinkle with Parmesan cheese and breadcrumbs. Add extra sage leaves on top and bake for 40 minutes.

Helpful Tips

Caramelize onions - stir onions occasionally but don't rush them; slow cooking develops deel flavor.
Slice thin and uniform - cut the butternut squash very thinly (⅛th of an inch) and as evenly as possible so it cooks consistently and layers neatly.
Use odds and ends first - place the irregular or smaller pieces on the bottom layer and reserve the most perfect half-moons for the top layer to make the gratin look appealing.
Brown the top - broil the last few minutes of cook time to brown and crisp the tops. But avoid overcooking the gratin so the squash doesn't become mushy but still has defined layers.

close up of butternut squash gratin in baking dish with serving spoon.

Serving Suggestions

I love serving this gratin at holidays as a fancy side dish but it will also work for any time of year.

Side dish: Serve this gratin with Yukon gold mashed potatoes or garlic green beans for an extra cozy, comforting meal.

Main dish: Pair this creamy butternut squash gratin with pork bites or rack of lamb for a hearty and satisfying dinner.

Fresh salads: Don’t forget to round out your meal with refreshing and vibrant salads. Romaine Salad and arugula salad are great options.

Condiments: Include probiotic-rich sides like fermented carrots or raw sauerkraut to add brightness and balance to the rich, creamy flavors.

More butternut squash gratin pairing suggestions:

Crispy Pork Bites
20 Minutes
Roasted Rack of Lamb with Garlic and Herb Crust
50 Minutes
Chunky Mashed Potatoes with Red Skin
30 Minutes
Chimichurri Chicken Thighs
1 Hours 10 Minutes

cut slice of butternut squash gratin on a plate with a fork.

Frequently Asked Questions

How do I store and reheat butternut squash gratin?

Gratin can be stored in an airtight container in the fridge for up to 4 days. Reheat in a 350°F (175°C) oven for 15-20 minutes until warmed through.

Can I freeze butternut squash gratin?

Yes, you can freeze it for up to 2 months; wrap tightly with plastic wrap and foil. Thaw in the refrigerator overnight and reheat in the oven, adding 5-10 extra minutes to ensure it is heated evenly.

Can I use milk instead of heavy cream?

Yes, but the sauce will be lighter and less rich. If you don't have heavy cream, I would use half-and-half but try to avoid using milk as the sauce will be too thin.

Looking for more related recipes? Here are some ideas:

Did you make this butternut squash gratin? Please leave a ⭐⭐⭐⭐⭐ recipe rating in the recipe card below and leave a review in the comments. Thank you!💚

Printable Recipe

butternut squash gratin in a baking dish on a kitchen towel.

Creamy Butternut Squash Gratin

Anya @ Prepare & Nourish

This scalloped butternut squash gratin is made with caramelized onions, sage, garlic, and thyme in a creamy sauce, layered and topped with Parmesan cheese and breadcrumbs then baked until golden and bubbling.

4.25 from 4 votes

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Prep Time 20

Cook Time 1

Resting Time 5

Total Time 1 25

Course Side Dish

Cuisine American

Servings servings

Calories 242 kcal

Equipment

Ingredients

1 butternut squash about 2 pounds
4 tablespoons butter
1 large onion sliced
4 garlic cloves
12 sage leaves cut into thin strips
1 tablespoon fresh thyme leaves
1 teaspoon sea salt
½ teaspoon black pepper
⅛ teaspoon nutmeg
1 cup heavy cream
½ cup grated Parmesan cheese
¼ cup breadcrumbs

Instructions

Preheat oven to 375°F. Peel 1 butternut squash and cut lengthwise. Remove seeds and pith. Thinly slice crosswise into ⅛-inch thick circles. You can also cut into half-moons.
Melt 4 tablespoons butter in a large skillet over medium heat. Add sliced 1 large onion sliced and season with salt to release juices. Cook until onions are caramelized (approximately 25 minutes), stirring occasionally.
Add 4 garlic cloves, 12 sage leaves, 1 tablespoon fresh thyme leaves, and season with 1 teaspoon sea salt, ½ teaspoon black pepper, and ⅛ teaspoon nutmeg and cook just until fragrant.
Reduce heat to medium-low and add 1 cup heavy cream. Whisk to combine everything and cook until cream sauce has thickened.
Spoon ¼ of the onion cream mixture to the bottom of the casserole dish. Arrange odds and ends of butternut squash slices across the dish, overlapping slightly. Spoon another ¼ of the cream onion mixture. Add a second layer of the butternut squash, followed by the 3rd ¼ of the onion cream mixture. Add the final layer of butternut squash, overlapping and pressing down so the top is flat all across the baking dish. Drizzle the remaining onion mixture.
Spread the cream onion sauce evenly to cover the squash. Sprinkle with ½ cup grated Parmesan cheese and ¼ cup breadcrumbs. Add extra sage leaves on top.
Cover with a piece of parchment paper then aluminum foil. Bake covered for 40 minutes on the middle rack. Remove the cover and bake for 10 more minutes to brown the tops. Remove from oven and allow to rest for 5 minutes for sauce to settle before serving.

Video

Notes

Note: Recipe was originally published in 2016 but has since been modified to omit arrowroot starch as video shows.

Storage: Gratin can be stored in an airtight container in the fridge for up to 4 days. Reheat in a 350°F (175°C) oven for 15-20 minutes until warmed through. You can also freeze it for up to 2 months; wrap tightly with plastic wrap and foil. Thaw in the refrigerator overnight and reheat in the oven, adding 5-10 extra minutes to ensure it is heated evenly.

Helpful Tips:

Caramelize onions - stir onions occasionally but don't rush them; slow cooking develops deel flavor.
Slice thin and uniform - cut the butternut squash very thinly (⅛th of an inch) and as evenly as possible so it cooks consistently and layers neatly.
Use odds and ends first - place the irregular or smaller pieces on the bottom layer and reserve the most perfect half-moons for the top layer to make the gratin look appealing.
Brown the top - broil the last few minutes of cook time to brown and crisp the tops

Nutrition

Nutrition Information

The information shown is an estimate provided for your convenience by an online calculator. It should not be considered as a substitute for a professional nutritionist's advice. See our complete Nutritional Information Disclaimer.

Keyword butternut squash, butternut squash gratin

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About Anya

Sharing wholesome recipes using seasonal ingredients and simplified methods since 2014. My hope is you'll feel right at home in this online kitchen, where you'll find real food recipes for real families.

Comments

4.25 from 4 votes (3 ratings without comment)