Savory Butternut Squash and Gruyère Bake

Warm, comforting, and irresistibly cheesy, this Savory Butternut Squash and Gruyère Bake is the ultimate fall side dish or vegetarian main.

Tender, sweet butternut squash and caramelized onions are folded into a rich, nutty brown-butter batter, seasoned with sage, thyme, and a hint of nutmeg and then layered with gruyère cheese.

Topped with melty Gruyère, it bakes to a golden, crisp perfection while staying soft and custardy inside — part gratin, part savory bread pudding.

Perfect for holiday dinners, Thanksgiving, fall gatherings, or cozy weeknight meals.

What ingredients do I need?

• Butternut Squash – provides natural sweetness and a creamy texture; can substitute with sweet potato, pumpkin, or kabocha squash.
• Sweet Onion – adds sweetness and depth of flavor when caramelized.
• Garlic – gives aromatic savory notes.
• Olive oil or butter – for slow-cooking onions; butter adds richness.
• All-purpose flour – provides structure; can use a 1:1 gluten-free flour blend for a GF option.
• Baking powder – helps the custardy batter rise slightly.
• Salt – enhances all flavors.
• Nutmeg – adds a warm, subtle spice that complements squash.
• Ground sage or finely chopped fresh sage leaves – earthy, savory herb that pairs with squash and brown butter.
• Thyme leaves (fresh or dried) – adds complexity and balances sweetness.
• Unsalted butter, browned – nutty flavor base for the batter; can substitute with regular melted butter if needed.
• Brown sugar – enhances the natural sweetness of squash and onions.
• Eggs – bind the batter and create a custardy texture.
• Heavy cream – adds richness and creaminess.
• Milk – adjusts batter consistency; can substitute with plant-based milk for dairy-free option.
• Grated Gruyère cheese – provides nutty, melty, and slightly sweet flavor; can substitute Swiss, Fontina, or Comté if desired.

Can I Substitute?

Yes! Like always though, any substitutions made to the recipe can result in a change in texture and/or flavor.

• Butternut squash: Sweet potato, pumpkin, or kabocha squash can work as alternatives.
• Gruyère cheese: Swiss, Fontina, or Comté are great substitutes if needed.
• Brown butter: Regular melted butter is fine if you’re short on time, but you’ll miss the nutty depth.
• Dairy-free: Use a plant-based milk (like oat or pea protein milk) and a vegan butter substitute; top with a vegan melting cheese.
• Gluten-free: Swap all-purpose flour with a 1:1 gluten-free flour blend.

• Refrigerator: Store covered for up to 4 days. Reheat in the oven at 325°F (165°C) for best texture.
• Freezer: Freeze unbaked for up to 2 months. Thaw overnight and bake as usual.
• Reheating tip: Cover with foil for the first 10 minutes to prevent over-browning, then remove foil to crisp the top.
• Pro leftovers tip! Cut this bake into 1″ thick pieces and sauté on each side on medium heat with a little olive oil, until crispy and browned. IT. IS. LIFE CHANGING.

But, I Still Have A Few Questions…

Can I make this ahead of time?
Absolutely! Prepare and assemble the bake the day before, cover tightly, and refrigerate. Remove from the fridge and bring to room temperature while the oven preheats and then bake, adding a few extra minutes if chilled.

Can I freeze it?
You can freeze fully assembled but unbaked for up to 2 months. Thaw overnight in the fridge before baking.

Can I use a different type of squash?
Yes — sweet potato, pumpkin, or kabocha squash are great alternatives. Adjust baking time as needed.

Can I make it vegan?
Yes — use plant-based milk, vegan butter, and a meltable vegan cheese. The texture will be slightly different but still delicious.

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Golden, cheesy, and cozy, this Savory Butternut Squash and Gruyère Bake is a fall and holiday favorite. Layers of sweet butternut squash and caramelized onions are folded into a nutty brown-butter batter, seasoned with sage, thyme, and a hint of nutmeg, then topped with melty Gruyère. It bakes to a golden, crisp perfection while staying soft and custardy inside — part gratin, part savory bread pudding. Perfect as a show-stopping holiday side dish or a comforting vegetarian main.

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Servings: 1 casserole

Ingredients

• ▢ 1 small butternut squash thinly sliced (about 3 cups)

Caramelized Onions

• ▢ 1 large onion thinly sliced
• ▢ 3 garlic cloves minced
• ▢ 1 tbsp olive oil or butter

Main Mixture

• ▢ 1½ cups all-purpose flour
• ▢ ½ tsp baking powder
• ▢ ¾ –1 tsp salt
• ▢ ¼ tsp nutmeg
• ▢ ½ tsp ground sage or 3–4 fresh leaves, finely chopped
• ▢ ½ tsp thyme leaves fresh or dried
• ▢ ½ cup 1 stick unsalted butter, browned and slightly cooled
• ▢ ¼ cup packed brown sugar
• ▢ 2 large eggs
• ▢ ⅓ cup heavy cream
• ▢ ¼ –½ cup milk add gradually for batter consistency
• ▢ 2 cups grated Gruyère cheese divided

Instructions

• Preheat oven to 350°F (175°C) and grease an 9×13” baking dish (or similar).

Caramelize the onions:

• In a skillet over medium-low heat, add olive oil, onions, and garlic. Cook slowly, stirring occasionally, for 15–20 minutes until golden and soft. Remove from heat and let cool slightly.

Prepare the brown butter:

• In a small saucepan, melt butter over medium heat until it foams and the milk solids turn golden brown and nutty, 5–7 minutes. Remove from heat and cool slightly.

Make the batter:

• In a large bowl, whisk together brown butter, brown sugar, eggs, heavy cream, and milk until smooth. Add in the flour, baking powder, salt, nutmeg, sage, and thyme. Stir until combined well— the batter should be thick but pourable.

Assemble:

• Fold in the sliced butternut squash and caramelized onions into the batter until coated well . Then add layers of the butternut squash slices into the baking dish. Add about 1/3 of the slices and then sprinkle with 3/4 cup of Gruyère cheese. Add another layer of squash and sprinkle another 3/4 cup of cheese, repeat this once more. Adding any extra batter to the top and spreading evenly. Sprinkle the remaining 1/2 cup cheese on top. (This step gets a little messy).

Bake:

• Bake uncovered for 55-60 minutes, until the top is golden and crisp, and a knife inserted in the center comes out mostly clean.

Cool and serve:

• Let rest for 10–15 minutes before slicing. Serve warm, optionally topped with crispy sage leaves or a drizzle of browned butter.

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