Creamy Quinoa Mac and Cheese Bake: Protein-Packed Comfort Dish

Creamy, hearty quinoa mac and cheese is a delicious twist on the classic. This version uses quinoa instead of pasta, a from-scratch cheese sauce, and sautéed greens for a comforting, gluten-free-friendly meal when prepared with a GF flour substitute.

quinoa mac and cheese in a dish topped with jalapenos and bacon

We love mac and cheese at Fit Foodie, and this quinoa version captures the same cheesy comfort without the noodles. It comes together on the stovetop in about an hour, with cooked quinoa, a rich cheese sauce, and fresh kale. Jalapeños and bacon add a nice flavor punch, but they’re optional — the result is just as creamy and satisfying as traditional mac and cheese.

Featured Comment

“Big fan! I love that at least if I’m eating an indulgent and cheesy meal, that it sneaks some healthy quinoa and kale in there. Great for a snowy day.” – Elizabeth

What You Need for Quinoa Mac and Cheese

The recipe has three main components: the cooked quinoa, a creamy cheese sauce, and optional add-ins. You’ll need:

Quinoa

Rinsed, uncooked quinoa is the base. Simmer it in chicken or vegetable broth until the liquid is absorbed.

Cheese Sauce

The sauce starts with sautéed onion, jalapeño (optional), and garlic, then a roux made with flour and olive oil. Whisk in milk and Greek yogurt, then stir in shredded cheddar until smooth and creamy.

Add-Ins

Fold chopped kale into the finished sauce for color and texture. Top servings with cooked, diced bacon if desired.

jalapeños, onions and garlic sautéing in a dutch oven

Quinoa Mac and Cheese Variations

Use the recipe as a template and try these simple swaps to match your taste or dietary needs:

Cheese: Swap cheddar for your favorite shredded cheese.

Greens: Substitute spinach for kale.

Spiciness: Control heat by removing jalapeño seeds for milder flavor, keeping some seeds for more heat, or omitting them entirely. Canned diced green chiles provide flavor with minimal spice.

Vegetarian: Use vegetable broth and skip the bacon topping.

Gluten Free: Replace the white whole wheat flour with a 1:1 gluten-free flour blend.

Spice Level

Jalapeños vary in heat. If unsure, reserve the seeds and taste the finished dish before adding them. Add seeds gradually until you reach the desired spice.

ingredients for jalapeno bacon quinoa mac and cheese, ready to be made in your kitchen

FAQ

Do you need to rinse the quinoa first?

Yes. Rinsing quinoa before cooking removes its natural bitter coating and improves texture.

Is this quinoa mac and cheese gluten free?

Not as written, but it can be made gluten free by using a 1:1 gluten-free flour blend in place of white whole wheat flour.

cheese sauce with fresh kale added in, ready to be mixed together for quinoa mac and cheese

Storage

Store leftovers in an airtight container in the refrigerator for up to 5 days. Freezing is not recommended: dairy-based dishes often become grainy after freezing and reheating.

Reheating Quinoa Mac and Cheese

Quinoa absorbs moisture after cooking, so add a splash of milk and reheat slowly over low heat to preserve a creamy texture. For best results, add 1 tablespoon of milk at a time to the leftovers until slightly loosened, transfer to an oven-safe dish, cover with foil, and warm at 350°F (about 10–20 minutes) until heated through.

quinoa mac and cheese in a dutch oven, ready to be served

Serving Suggestions

This quinoa mac and cheese is great on its own or paired with roasted vegetables and a simple protein. Try it with roasted broccoli or garlic-glazed carrots and grilled chicken or slow-roasted pork shoulder.

Quinoa Mac and Cheese

Homemade quinoa mac and cheese offers the same comforting flavors as classic mac, with quinoa standing in for noodles for a hearty, wholesome dish.
By: Emily Richter
Prep: 30 mins
Cook: 30 mins
Total: 1 hr
Servings: 6
quinoa mac and cheese

Ingredients

  • 1.5 cups uncooked quinoa, rinsed
  • 3 cups chicken or vegetable broth
  • 1/4 cup + 1 tablespoon olive oil, divided
  • 1/2 medium white onion, minced
  • 1/2 tablespoon minced garlic
  • 1/4 cup minced jalapeño peppers, seeded (about 2 small or 1 large) — optional
  • 1/3 cup white whole wheat flour (or 1:1 GF blend to make gluten free)
  • 2 cups 2% milk
  • 1/2 cup plain Greek yogurt
  • 3 cups shredded cheddar cheese
  • 1/2 teaspoon salt
  • 1/4 teaspoon ground pepper
  • 4 cups chopped kale, packed
  • Diced cooked bacon, for serving (optional)

Instructions

Make the Quinoa

  • Combine the uncooked quinoa and broth in a medium saucepan. Bring to a boil over medium-high heat. Once boiling, cover and reduce heat to low. Simmer about 15 minutes or until the broth is absorbed. Remove from heat and set aside.

Make the Cheese Sauce

  • Heat 1 tablespoon olive oil in a large pot or Dutch oven over medium-high heat. Add the onion and sauté 1–2 minutes until fragrant. Add the garlic and sauté until the onion is translucent. Stir in minced jalapeños and cook 2–3 minutes more (omit or reduce for less heat).
  • Add 1/4 cup olive oil to the pot and sprinkle in the flour. Stir with a wooden spoon until a paste forms. Whisk in the milk and cook over medium-high heat until the mixture thickens, about 2–3 minutes. Whisk in the Greek yogurt, then add the cheddar a half cup at a time, whisking until melted and smooth. Season with salt and pepper.

Make the Quinoa Mac and Cheese

  • Once the cheese sauce is smooth, stir in the kale and cook until wilted. Stir in the cooked quinoa until well combined and heated through.
  • Serve immediately, topped with cooked bacon if desired.

Tips & Notes

  • Storage: Refrigerate leftovers in an airtight container up to 5 days. Freezing is not recommended because dairy can change texture after thawing.
  • Jalapeños: Adjust spice by omitting peppers, using diced green chiles, or adding seeds for extra heat.
  • Bacon: Optional — omit for a vegetarian version.

Nutrition

Calories: 521 kcal, Carbohydrates: 38 g, Protein: 7 g, Fat: 27 g, Fiber: 4 g, Sugar: 7 g

Nutrition information is an approximation.