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Quinoa Egg Muffins

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Quinoa egg muffins a very easy breakfast recipe made with cooked quinoa, eggs, broccoli, ham and cheese.

These savory muffins can be put together fast using cooked quinoa as the base. In less than 30 minutes you’ll have 12 grab-and-go muffins for meal prep breakfast recipes throughout the week!

quinoa egg muffins stacked on a plate

Veggie Quinoa Egg Muffins

  • Perfect for busy mornings, these quinoa egg cups are so easy to prep and take less than 10 minutes.
  • Quinoa is a healthy whole grain and high in protein. It’s an easy way to avoid gluten and regular all-purpose flour.
  • With simple wholesome ingredients that are budget-friendly, you really can’t go wrong here.
  • Traditional muffins use flour, but this one replaces with healthy cooked quinoa which is low carb and high in protein.
  • Serve with your salsa and a healthy homemade smoothie for the perfect way to start the day.
  • This recipe can also be added to mini muffin tins for toddler food.
  • If you like easy grab-and-go breakfast ideas, then try our popular 6 Healthy Overnight Oat Recipes or easy chia pudding recipes.
quinoa breakfast muffins cooked in a muffin pan

Recipe Ingredients

  • QUINOA: These muffins use 2 cups of cooked white quinoa.
  • EGGS: You’ll need 6 eggs for the recipe.
  • CHEDDAR CHEESE: You can use grated sharp cheddar cheese or any other kind like mozzarella, marble, feta cheese and parmesan cheese.
  • BROCCOLI: You’ll need one cup of broccoli florets, chopped into tiny pieces. Use fresh or frozen to save time.
  • HAM: This recipe uses 1 cup of ham. Use leftover ham or deli ham.
  • SPICES: To add flavor, simple spices including garlic powder, onion powder, dried parsley, salt and pepper are used.
  • VARIATIONS: Substitute with fresh vegetables like chopped bell pepper, green onions, cooked asparagus, shredded carrots or brown rice.
three quinoa breakfast muffins stacked on top of eachother

How To Make Quinoa Egg Muffin Cups

  1. First you’ll need to cook the quinoa. For this recipe you’ll need 2 cups. This is about ⅓ cup dry quinoa + 1 ⅓ cup water to make. But I like to make a bigger batch of quinoa for lunches and dinner throughout the week.
  2. Beat eggs in a medium bowl, then add spices according to full instructions in the recipe card below.
  3. Add cooked quinoa, broccoli florets, chopped ham, cheddar cheese and the beaten eggs to a large mixing bowl. Mix with eggs and spices.
  4. Add to a greased muffin pan and bake until cheese melts and edges are golden.

I like to spread a bit of avocado mayonnaise onto my quinoa muffins, but you could use salsa, ketchup, hot sauce, plain greek yogurt, or cottage cheese.

Store leftover quinoa breakfast muffins in an airtight container in the fridge up to 4-5 days. These muffins also freeze well! I recommend wrapping each one in parchment or plastic wrap, and placing them in a large airtight freezer bag.

When you’re ready to eat, just grab one from the freezer and pop it in the microwave or toaster oven (remove the plastic wrap) for the perfect grab-and-go breakfast.

close up of broccoli quinoa muffins in a muffin pan

More Perfect Breakfast Recipes

Quinoa Egg Muffins Recipe

These savory breakfast muffins can be put together using a few simple ingredients and cooked quinoa as the base.
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Prep Time: 10 minutes
Cook Time: 25 minutes
Servings: 12 mufifns



  • Preheat the oven to 350°F.
    Cook quinoa according to package instructions (⅓ dry quinoa + 1 ⅓ cup water will make about 2 cups cooked quinoa).
  • Beat 6 eggs with a fork in a bowl.
  • Mix in the garlic powder, onion powder, dried parsley, salt and pepper.
  • Add the cooked quinoa, broccoli florets, chopped ham, and cheddar cheese to a large bowl.
  • Add the egg mixture and stir everything together.
  • Spray a muffin pan with nonstick cooking spray or use a muffin liner.. I use avocado oil spray.
  • Scoop the quinoa mixture into each muffin cup. Sprinkle the tops with more cheese if desired.
  • Bake muffins for 22-25 minutes. Let cool 10 minutes, then transfer to a rack to cool completely.
  • These muffins can be stored in the fride for up to 1 week, or freezer for up to 3 months.
    To Serve: Wrap one in a paper towel and reheat in the microwave for 1-2 minutes. Serve with salsa, avocado mayonnaise or any other sauce you enjoy.


Calories: 128kcal | Carbohydrates: 7g | Protein: 9g | Fat: 7g | Saturated Fat: 3g | Polyunsaturated Fat: 1g | Monounsaturated Fat: 3g | Trans Fat: 1g | Cholesterol: 96mg | Sodium: 218mg | Potassium: 150mg | Fiber: 1g | Sugar: 1g | Vitamin A: 238IU | Vitamin C: 7mg | Calcium: 73mg | Iron: 1mg

The nutritional information provided is an estimate and is per serving.

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