Broccoli Cheese Egg Muffins are fluffy inside, with golden cheese crust on top and are perfect for meal prep!

Wondering what other ways you can spruce up your morning eggs? Check out these quinoa egg muffins, cottage cheese egg bites or Instant Pot egg bites.

Broccoli cheese egg muffins on platter.

These broccoli cheese egg muffins are so versatile they are perfect for everyone!

From a post workout snack and an easy make ahead breakfast, to toddler meals and special occasion brunches. There’s always a place for them and best of all, they’re ridiculously easy to make.

Like a little portable frittata!

This recipe calls for broccoli and cheese, mozzarella or a really good sharp cheddar is usually my favorite.

However, you can add whatever veggies you’ve got in the fridge and whatever cheese your family likes.

This recipe is a perfect contender for a leftover quinoa or a total fridge cleanout.

Why You’ll Love These Egg Muffins

Below are just a few reasons why I love them for breakfast, lunch, or snack!

  • Freezer friendly: I like to make a couple of batches and freeze some for later. This way I know I’ve got something to grab and go during my morning rush.
  • Packed with nutrients: Low in carbs and packed with protein, omega 3s, vitamins, and minerals to keep me going until my next meal.
  • Customizable: A great way to use up leftover veggies. You can even make a few different varieties in one batch!
  • Great texture and flavor: The extra egg whites keep them nice and fluffy, while the quinoa helps to ground them with added substance. So much goodness in one little egg cup!

Ingredients Needed and Notes

Take my recipe and run with it! Get creative with what you add to yours.

  • Large eggs & egg whites: I find using both gives it the perfect consistency. Moisture and richness, but also with a light and fluffy texture.
  • Cottage cheese: You can also use ricotta or crumbled feta cheese if you’d prefer. Cottage cheese has a lot of protein, however, feta delivers a saltier flavor.
  • Shredded cheese: Any kind you like. Mozzarella is always nice, as is cheddar, Swiss, gruyere, or Parmesan.
  • Seasoning: Onion or garlic powder, salt, pepper, and red pepper flakes are all you need for flavoring.
  • Cooked quinoa: High in fiber and antioxidants, you can make this ahead of time and speed things up even more.
  • Veggies: Raw broccoli coarsely chopped. To reduce waste, you can use the stalk as well as the florets if you’d like.
  • Fresh herbs: Green onion and parsley add a nice mild pungency to the broccoli egg muffins with cheese.

How to Make Broccoli Cheese Egg Muffins

Broccoli cheese egg muffins combined in a bowl and then baked in a muffin tin.
  1. Whisk eggs and add cottage cheese. Crack your eggs into a large mixing bowl and whisk those along with the egg whites for 30 seconds. Add in the cottage cheese and all the seasoning and stir to combine.
  2. Throw in your veggies. Last, you’ll want to toss in the quinoa, veggies, herbs, and green onions. Mix everything to combine.
  3. Fill the muffin pan. Grab your prepared muffin tin which should have muffin liners as well as cooking spray if you don’t have a silicone muffin tin. Fill each groove with the egg mixture about 3/4 full. Sprinkle each one with extra shredded cheese if you’d like and bake for 20 minutes in preheated oven at 350 degrees F.
  4. Optional broil. If you want a little more golden crust on top, place it under the broiler until golden brown.
  5. Allow them to cool for about 10 minutes at least. These can be served hot or cold!

Variations and Substitutions

  • Broccoli will be perfectly tender but still have a bite to it. You can also use snap peas, asparagus, sauteed mushrooms, or bell pepper.
  • Fresh herbs add a ton of flavor. I used parsley and green onion but dill would be amazing too.
  • Replace cottage cheese with 1/4 cup of salty briny feta or mild goat cheese.
  • Add some extra protein like diced ham, cricpy baked bacon, shredded chicken, or Italian sausage.

Tips for Best Results

  • Keep them from sticking. Egg muffins stick no matter what kind of magic non-stick pan you’ve got. Also, not to mention, cooking with Teflon cookware that has a non-stick coating isn’t exactly healthy. Make sure you use either a silicone muffin pan or line it with unbleached parchment muffin liners and use a cooking spray like Misto.
  • Egg whites are a bonus. Egg yolks are full of nutrients like vitamin B, folate, carotenoids, protein, and Omega-3 fats. The addition of egg whites can help lighten it up and increase the fluffy texture, but it’s not necessary. It’s up to you!
  • Chop your veggies small. To be able to get enough of the veggies, cheese, and seasoning in every bite, you want to make everything small enough to fit. You also want to make sure it’s not overpowering the egg, so that it ends up being more veggies than eggs!

Storage Tips

  • To store: Egg muffins keep fresh in the fridge for up to 5 days for an entire week of healthy grab-and-go breakfasts. I like to use glass containers just because the chemicals from plastic containers can leak into your food.
  • To freeze: Completely cool muffins, then freeze in an airtight container for up to 3 months.
  • Thaw: On the counter for 2-3 hours or in the fridge overnight. You can also defrost in a microwave for a few minutes, depending on your microwave, and check muffins often.
  • To reheat: Use a toaster oven, a regular oven at 400 degrees F for 10 minutes, or a quick zap in the microwave.


How do you cook quinoa?

Here is how to cook quinoa. Combine 1 cup dry and unrinsed quinoa, 2 cups cold water and pinch of salt in a medium pot. Bring to a boil, cover and cook 12 minutes. Remove from heat and let stand for 5 minutes, then fluff with a fork.

Can I omit the quinoa?

I think you can but I haven’t tried. You might also have to bake the muffins a bit longer so they set. Please let me know if you do.

Do I have to cook broccoli?

No. Broccoli is chopped.

Can I use only egg whites?

Sure. Total amount will be 2 1/4 cups egg whites. Omit the eggs.

More Healthy Egg Recipes to Try

Be sure to browse these 30 healthy egg recipes as well.

A sliced broccoli cheese egg muffin on platter with whole egg muffins in background.

Broccoli Cheese Egg Muffins

Broccoli Cheese Egg Muffins are fluffy inside, with golden cheese crust on top and are perfect for meal prep!
5 from 24 votes
Servings 12 muffins
Calories 93
Diet Gluten Free
Prep Time 10 minutes
Cook Time 20 minutes
Cooling Time 10 minutes
Total Time 40 minutes



  • Preheat oven to 350 degrees F and place unbleached muffin liners into a 12 muffin tin and spray with cooking spray. Alternatively, you could use silicone muffin tin.
  • In a large mixing bowl, whisk eggs and egg whites for 30 seconds. Add cottage cheese, mozzarella cheese, onion or garlic powder, salt, pepper, red pepper flakes and stir to combine. Add quinoa, broccoli, parsley and green onions, and mix.
  • Fill each muffin with egg mixture 3/4 full and sprinkle with extra mozzarella cheese on top (optional). Bake for 20 minutes and then broil until golden brown crust appears (optional).
  • Remove from the oven and let cool about 10 minutes. Serve hot or cold.


  • Store: Refrigerate in an airtight container for up to 5 days. Reheat in microwave for easy breakfast on-the-go or a snack.
  • Freeze: In an airtight container for up to 3 months. Defrost in a microwave or thaw on a counter.
  • Here is how to cook quinoa: Combine 1 cup dry and unrinsed quinoa, 2 cups cold water and pinch of salt in a medium pot. Bring to a boil, cover and cook 12 minutes. Remove from heat and let stand for 5 minutes, then fluff with a fork. You can also make Instant Pot quinoa.
  • Use all eggs: 9 large eggs in total and omit egg whites.
  • Use all egg whites: Total amount will be 2 1/4 cups. Omit the eggs.


Serving: 1muffin | Calories: 93kcal | Carbohydrates: 6g | Protein: 7g | Fat: 5g | Saturated Fat: 2g | Cholesterol: 127mg | Sodium: 199mg | Fiber: 1g | Sugar: 1g
Course: Breakfast
Cuisine: North American
Author: Olena Osipov
Did you make this recipe?Mention @ifoodreal or tag #ifoodreal!

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About Olena

Welcome! I grew up in Ukraine watching my grandma cook with simple ingredients. I have spent the last 11 years making it my mission to help you cook quick and easy meals for your family!

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  1. 5 stars
    Looks yummy! Trying these now…they are in the oven 🙂 Question – would this recipe work if I used muffin cups inside the muffin pan?

    1. Yes. I used thin almost wax paper like liners in Sundried Tomato Spinach Quinoa ️muffins and it almost worked. Just let them cool down completely. You can search my site to see how those look. Sorry can’t insert link on my phone.

  2. 5 stars
    These look and sound perfect. But I’m a little confused about the egg whites. 1 + 1/2 cup egg whites? Is that another whole egg (on top of the 3 large) plus 1/2 cup egg whites or is it 1.5 cups egg whites? How many separated eggs does it take to total 1.5 cups of whites?

    1. I use egg whites in a carton. My best advice is to separate the eggs until you reach a required amount of egg whites.

    1. Awesome! These are very handy for busy mornings. I’m making 2 batches today and freezing. I love these! It’s so hard to come up with a quick breakfast that’s low in sugar and not overdone with carbs. Bingo here!

  3. 5 stars
    I love your Pinterest page. Wonderful food selections. My daughter told me about Quinoa. This recipe sounds great and easy to make and that they can be frozen. Will be sending this one to my daughter. I found your pans on Amazon. Just what I was looking for. Thanks.

    1. Hi BJ. Awe, thank you! Yes, you need a good muffin tin otherwise the muffins will stick. Like the eggs get burnt on a low quality or an old skillet. You will love it and these muffins. And quinoa is the new brown rice.

  4. 5 stars
    Wow, these look great, and what a great breakfast idea for something that can be frozen and then heated up when you’re on the go! Looks mighty tasty 🙂

  5. 5 stars
    I have made something similar before but I didn’t use any quinoa. I love this variation and the fact that you also used egg whites together with regular eggs is great. More protein and less cholesterol 🙂

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