Dinner

Cheesy Broccoli Cheddar Spaghetti Squash Recipe

ByMaya Arden March 4, 2026March 4, 2026

Introduction

This Cheesy Broccoli Cheddar Spaghetti Squash is a comforting, gluten-free twist on classic mac and cheese. Roasted spaghetti squash strands are coated in a creamy cheddar sauce and combined with tender broccoli florets for a delicious, satisfying meal.

Two halves of a baked spaghetti squash sit on a silver tray, each filled with a golden layer of melted cheese that is bubbly and browned in spots. Inside the cheese are bright green broccoli florets, slightly roasted with a soft texture. A spoon lifts a piece from the front half, showing gooey strings of melted cheese stretching from the squash to the spoon. The squash's pale yellow flesh is soft and slightly textured, visible beneath the cheese layers. The setting is on a white marbled surface. photo taken with an iphone --ar 4:5 --v 7

Ingredients

1 medium spaghetti squash (about 2 1/2 lb.)
1 tbsp. neutral oil

1 3/4 tsp. kosher salt, divided
6 oz. broccoli, cut into 1″ florets (about 1 1/4 cups)

1 tbsp. plus 1/4 cup water, divided
3 tbsp. unsalted butter

1/2 yellow onion, finely chopped
3 garlic cloves, minced
1 tbsp. all-purpose flour

1/2 cup whole milk
4 oz. cheddar, shredded, divided (about 1 cup)

Instructions

Step 1: Preheat the oven to 400°F and arrange a rack in the center. Cut the spaghetti squash in half lengthwise and scrape out the seeds. Rub the inside of each half with oil and season with 1 teaspoon of salt. Place the squash cut side down on a baking sheet.

Step 2: Roast the squash until tender and browned, about 35 to 45 minutes. Allow to cool slightly.
Step 3: Meanwhile, place broccoli florets in a medium heatproof bowl. Season with 1/4 teaspoon salt and pour 1 tablespoon water into the bowl. Cover and microwave for 1 minute. Stir and continue microwaving in 30-second increments until broccoli is bright green and fork-tender, 30 seconds to 1 minute more. Let cool slightly.
Step 4: In a large skillet over medium heat, melt butter. Add onion and season with 1/2 teaspoon salt. Cook, stirring occasionally, until the onion is tender and sweet, about 7 to 8 minutes. Add garlic and cook for 1 minute more until fragrant.

Step 5: Stir in flour and cook, stirring, until a bubbling paste forms on the skillet bottom, about 1 minute. Slowly whisk in milk and the remaining 1/4 cup water. Bring to a simmer over medium-high heat and cook, stirring occasionally, until thickened, 1 to 2 minutes.
Step 6: Remove skillet from heat and fold in 3 ounces of shredded cheddar until smooth. Taste and add salt if needed.
Step 7: Use two forks to shred spaghetti squash strands from the shells. Measure out 3 cups and add them to the skillet. Toss in broccoli and coat everything evenly in the cheese sauce.

Step 8: Spoon the cheesy squash mixture back into the squash shells and top with the remaining 1 ounce of cheddar.
Step 9: Set your oven to broil and broil the stuffed squash, watching closely, until the cheese melts and blisters, about 1 to 2 minutes.

Tips & Variations

For a richer sauce, swap whole milk for half-and-half or add a splash of cream.

Add a pinch of smoked paprika or cayenne pepper for a subtle smoky or spicy kick.
Swap broccoli for other vegetables like cauliflower or roasted Brussels sprouts.
Use sharp or extra-sharp cheddar for a bolder flavor.

Storage

Store leftover cheesy spaghetti squash in an airtight container in the refrigerator for up to 3 days. Reheat gently in the microwave or in a skillet over low heat to avoid drying out the squash. The broiled cheese topping might lose its crispness when reheated.

How to Serve

A white plate holds a hollowed-out spaghetti squash that is cooked and split in half, showing three main layers: the top layer is golden yellow with light browning at the edges, the middle layer contains small pieces of green broccoli mixed with melted, slightly browned cheese, and the bottom layer is soft, shredded pale yellow squash strands. A metal fork is stuck into the squash near the middle layer, pulling up some of the shredded strands. The background is a white marbled texture. Photo taken with an iphone --ar 4:5 --v 7

Serve this delicious recipe with your favorite sides.

FAQs

Can I prepare the spaghetti squash ahead of time?

Yes, you can roast and shred the spaghetti squash up to two days in advance. Store it in an airtight container in the refrigerator until ready to assemble and bake.

Is this recipe gluten-free?

This recipe uses all-purpose flour to thicken the cheese sauce, which contains gluten. To make it gluten-free, substitute the flour with a gluten-free all-purpose flour blend or cornstarch.