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.
½cup1 stick unsalted butter, browned and slightly cooled
¼cuppacked brown sugar
2large eggs
⅓cupheavy cream
¼–½ cup milkadd gradually for batter consistency
2cupsgrated Gruyère cheesedivided
Instructions
Preheat oven to 350°F (175°C) and grease an 9x13” 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.