Butternut Squash and Caramelized Onion Flatbread Pizza Recipe

This Butternut Squash & Caramelized Onion Flatbread Pizza is an ideal autumn pizza—roasted butternut squash layered over fresh mozzarella, sweet caramelized onions, and fresh sage, finished with a peppery arugula toss. It works well for weeknight dinners or sliced into small pieces for seasonal gatherings.

Slices of butternut squash and caramelized onions on a wooden board topped with arugula.

I prefer thin-crust pizzas, so flatbreads are my go-to when I want a quick, flavorful pie. This version begins with roasted butternut squash and slowly caramelized onions. Layer the cooked squash and onions over flatbread with fresh mozzarella and sage, bake until the cheese melts, then dress baby arugula with olive oil and balsamic and pile it on top. The result is bright, savory, and perfect for fall.

slices of flatbread pizza topped with butternut squash, caramelized onion, and arugula on a wooden board

Ingredients

  • 1 large butternut squash, peeled, seeded, and cubed
  • 4 tablespoons extra virgin olive oil, divided
  • Salt and pepper
  • 2 tablespoons butter
  • 1 large yellow onion, thinly sliced
  • 1 package flatbread (2 flatbreads)
  • 2 cups freshly shredded mozzarella
  • 1/4 cup fresh sage leaves
  • 3 cups baby arugula
  • 1/3 cup balsamic vinegar

Butternut squash and onion flatbread pizza on a wooden cutting board

Instructions

  1. Preheat the oven to 425°F (220°C). Line a baking sheet with parchment paper. Toss the cubed butternut squash with 2 tablespoons of olive oil, salt, and pepper. Spread in a single layer and roast 25–35 minutes, until tender. Remove and set aside.
  2. While the squash roasts, heat a sauté pan over medium heat and melt 2 tablespoons butter. Add the sliced onions with a pinch of salt and cook, stirring occasionally, until golden and caramelized, about 10–15 minutes. Remove from heat.
  3. Reduce oven heat to 375°F (190°C). Place the flatbreads on a baking sheet. Divide the shredded mozzarella across the flatbreads, then top with caramelized onions, sage leaves, and roasted squash. Season with a little more salt if desired.
  4. Bake about 8–12 minutes or until the flatbreads are heated through and the cheese has melted. Remove from the oven and cut into slices.
  5. In a bowl, toss the arugula with the remaining 2 tablespoons olive oil, balsamic vinegar, and salt and pepper to taste. Serve the tossed arugula on top of the warm slices or alongside as a fresh salad.

Tips & Variations

  • Make-ahead: Roast the squash and caramelize the onions in advance; refrigerate until ready to assemble.
  • Shortcuts: Pre-cut butternut squash from the produce section saves prep time.
  • Cheese swaps: Try fontina or gruyère for a more pronounced flavor instead of mozzarella.
  • To add protein: Scatter crumbled bacon, pancetta, prosciutto, or shredded chicken before baking.
  • Additional toppings: Shaved Brussels sprouts, mushrooms, or fresh thyme pair well with these fall flavors.
  • Serving: This flatbread is great as a main for a casual dinner or sliced into bite-size pieces for an appetizer at autumn gatherings.

Flatbread pizza topped with cubed butternut squash, onions, and fresh arugula

Slices of butternut squash and caramelized onions on a wooden board topped with arugula.
Yield: 3-4 servings

Butternut Squash & Caramelized Onion Flatbread Pizza

Prep Time
25 minutes
Cook Time
1 hour
Total Time
1 hour 25 minutes

Ingredients

  • 1 large butternut squash; peeled, seeded, and cubed into small pieces
  • 4 tablespoons extra virgin olive oil, divided
  • Salt & pepper
  • 2 tablespoons butter
  • 1 large yellow onion, thinly sliced
  • 1 package flatbread (2 flatbreads)
  • 2 cups freshly shredded mozzarella
  • 1/4 cup fresh sage leaves
  • 3 cups baby arugula
  • 1/3 cup balsamic vinegar

Instructions

  1. Preheat oven to 425°F. Line a baking sheet with parchment and roast the cubed squash tossed with 2 tablespoons olive oil, salt, and pepper until tender, about 25–35 minutes. Set aside.
  2. Caramelize the onions: melt 2 tablespoons butter in a sauté pan over medium heat, add the sliced onions and a pinch of salt, and cook 10–15 minutes until golden. Remove from heat.
  3. Lower oven to 375°F. Arrange flatbreads on a baking sheet, top with shredded mozzarella, caramelized onions, sage leaves, and roasted squash; season lightly with salt.
  4. Bake 8–12 minutes until warmed through and cheese is melted. Slice and serve.
  5. Toss arugula with remaining 2 tablespoons olive oil, balsamic vinegar, salt, and pepper. Spoon over each slice or serve on the side.

Nutrition Information:

Yield:

4

Serving Size:

1/2 flatbread pizza (out of 2 whole)

Amount Per Serving:
Calories: 417
Total Fat: 28g
Saturated Fat: 11g
Trans Fat: 1g
Unsaturated Fat: 16g
Cholesterol: 43mg
Sodium: 539mg
Carbohydrates: 28g
Fiber: 3g
Sugar: 7g
Protein: 14g

© Stephanie
Category: Pizzas

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Butternut Squash & Caramelized Onion Flatbread Pizza