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a stack of quinoa egg muffins

Quinoa Egg Muffins ~ A Make-Ahead Breakfast

  • Author: amycaseycooks
  • Total Time: 35 minutes
  • Yield: 12 servings 1x


Quinoa Egg Muffins. These grab and go savory muffins are perfect for busy mornings. The protein packed muffins are loaded with quinoa, eggs, spinach, onion, bacon, and Gruyere and Parmesan cheese. Make a batch and breakfast is ready and waiting for you.


Units Scale
  • cooking spray
  • 3/4 cup dry quinoa
  • 1 tablespoon salted butter
  • 1 cup diced onion
  • 4 slices of bacon, diced
  • 3 garlic cloves, minced
  • 9 large eggs
  • 10 ounces frozen chopped spinach, cooked, drained and cooled
  • 1 1/2 cups shredded Gruyere cheese
  • 1/2 cup grated Parmesan cheese
  • 2 teaspoons Dijon mustard
  • 1 teaspoon kosher salt
  • 1/4 teaspoon pepper


  1. Prep the muffin pan: Preheat the oven to 350 degrees F. Generously coat a muffin pan with cooking spray and set aside.
  2. Cook the quinoa: In a small pot over medium heat, add the quinoa and 1 1/2 cups water. Bring to a boil. Then turn down the heat to low, cover to pot, and simmer for 14 to 15 minutes. All the water should be absorbed and the quinoa fluffy. Place the quinoa in a bowl to cool.
  3. Sauté the onion and bacon: In a large sauté pan over medium low heat, add the butter, onion and bacon. Sauté for 6 to 8 minutes. Add the garlic and sauté for about 30 more seconds. Drain off any bacon grease. Put the onion, bacon, and garlic in a bowl to cool.
  4. Mix the muffins: In a large bowl, crack the eggs and whisk until well combined. Add the cooked quinoa, spinach, both cheeses, the sauteed onion, bacon and garlic, Dijon mustard, kosher salt and pepper. Stir to thoroughly combine the ingredients.
  5. Fill the muffin pan: Generously fill the muffin cups with the quinoa and egg muffin mixture. The muffins only puff up a small amount so don’t worry about filling the muffin cups too full. This large cookie scoop is ideal for filling the pan.
  6. Bake the muffins: Place the muffin pan in the oven and bake the muffins for 18 to 20 minutes. The muffins are done when the center in firm to the touch.
  7. Cool the muffins: Remove the muffin pan from the oven and place on a cooling rack. Let the muffins cool about 5 minutes before removing from the pan.
  8. Unmold the muffins: Run a sharp knife around the edge of each muffin and carefully lift out of the pan. Serve immediately or cool slightly and serve at room temperature.


  • Spray the muffin pan: Generously coat each muffin cup and the top of the muffin pan to make removing the quinoa egg muffins a snap.
  • Drain the spinach: After cooking the spinach, thoroughly squeeze out as much of the water as possible. Any extra liquid will make the quinoa egg muffins watery.
  • Fill up those cups: The muffins only puff up a small amount so don’t worry about filling the muffin cups too full. This large cookie scoop is ideal for filling the pan.
  • Cool the muffins: Allow the muffins to cool about 5 minutes in the pan for easy removal.
  • Make ahead directions: Store cooled muffins in an air tight container (I love these glass storage containers) in the refrigerator for up to 5 days or in the freezer for up to 2 months. To reheat refrigerated or frozen muffins, place in the microwave and heat on 70% power at 30 second intervals until they are heated through.
  • Prep Time: 15 minutes
  • Cook Time: 20 minutes
  • Category: breakfast
  • Method: bake in oven
  • Cuisine: American


  • Serving Size: 1 muffin
  • Calories: 225
  • Sugar: 1 g
  • Sodium: 554 mg
  • Fat: 13.5 g
  • Saturated Fat: 6 g
  • Unsaturated Fat: 0 g
  • Trans Fat: 0 g
  • Carbohydrates: 10 g
  • Fiber: 1.6 g
  • Protein: 16.5 g
  • Cholesterol: 168 mg

Keywords: quinoa egg muffins, egg cups, breakfast recipes, make ahead breakfast