Savory, nutrient-dense, and naturally low-carb, these Gluten-Free Egg Muffin Cups are the perfect meal prep breakfast for busy mornings. Dairy-free but lightly cheesy and baked in a muffin tin, they’re easy to grab on your way out the door.

"I really like the addition of nutritional yeast! Never thought about that for a recipe like this but it sounds genius to me! I am going to try these with unsweetened coconut milk!" -GiGi Eats
A Quick Look At The Recipe
- ⏲️Ready In: 55 Minutes
- 👪Serves: 12 Muffins
- 🍽 Calories and Protein: 53 kcals and 6 grams of protein
- 📋Main Ingredients: Eggs, broccoli and spinach, almond milk, nutritional yeast, garlic powder, and turmeric.
- 📖 Dietary Notes: Dairy-free, gluten-free, keto, paleo, and Whole30.
- ⭐ Why You'll Love It: These gluten-free keto egg muffins are protein-packed, easy to meal prep, and perfect for busy mornings.
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For busy mornings when cooking isn’t an option, these dairy-free egg muffins make an easy high-protein breakfast you can grab and go. They’re packed with nourishing ingredients and a simple way to start your day with protein, especially if you’re working toward higher protein goals like learning how to eat 100g of protein a day.
They’re also perfect for meal prep (similar to this carnivore casserole or dairy-free mini quiche) since they freeze and reheat beautifully. I make them often for my kids, so there’s always something nutritious ready in the morning. Need more ideas? The Rise and Chill Breakfast E-Book includes 26 high-protein meal prep breakfasts plus a 5-day quick start guide to help simplify hectic mornings.
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💭Why You'll Love This Recipe
Easy-to-make: All you need to do is whip everything up in a bowl, portion, and bake these egg muffins to come together.
Nutritious meal prep: The egg muffin cups can be made in advance and reheated to make mornings a little easier, similar to this dairy-free egg casserole.
Versatile: With simple swaps, you can vary the flavor of the healthy, gluten-free egg muffin cups to suit your preference, just like this with healthy breakfast hash.
Ingredients and Substitutions

Most of the ingredients needed are basic kitchen staples or high protein food staples, and you already have them on hand.
- Egg whites: These have more protein in them than regular eggs so they're a good addition. Make sure to use the cartoned egg whites.
- Seasoning: All the seasonings can be adjusted to suit your personal preference.
- Nutritional yeast: all the cheesy flavor without all the cheese! This is one of my dairy-free swaps because it gives a big nutrient bang in just a few tablespoons.
- Looking for a vegan option? Check out these vegan egg muffins.
See the recipe card for full information on ingredients and quantities.
Flavor Variations
Veggies: Skip the broccoli and add in chopped bell peppers or cauliflower.
Immune-boosting: Opt to add sliced leek in place of spinach.
Protein: Add some chopped bacon or gluten-free sausage into the egg mixture for additional protein and savory flavor!
How To Make Gluten-Free Egg Muffin Cups

Step 1: Whisk together the eggs, egg whites, baking powder, and seasonings.

Step 2: Add in the vegetables and dairy-free milk.

Step 3: Portion the egg mixture into a silicone muffin pan (or use liners) and bake them until cooked through.
Important Teaching Tips
Either bake the egg muffins in a silicone muffin pan or place silicone liners in a traditional muffin pan. This makes them easier to remove as otherwise they stick to the sides.
Know that any vegetables will work for the recipe, but chop them finely so that they fully cook and don't create air pockets.
Serve them alongside a dairy-free yogurt parfait or low calorie baked oats so that you hit your protein goals.
Don't overcook the egg muffins. Egg muffins become rubbery when they’re cooked too long or at too high a temperature. Bake them just until the centers are set and still slightly soft; they’ll continue to firm up a bit as they cool.
How To Store and Meal Prep Them
Store the egg cups in the fridge for 3-4 days in an airtight container.
To reheat egg muffins: Let them thaw in the fridge if frozen, then cook them in the oven on super low or pop them in the microwave briefly.
Meal prep them: Pop the muffins out of the molds and turn them sideways. Then, place the entire muffin tin in the freezer for 30 minutes. Remove it and place the muffins into a freezer-safe bag and store them in the freezer for up to 2 months. Doing it this way just ensures they don't stick together as much, and you can remove them one by one to enjoy.
Gluten-Free Egg Muffin Cups FAQs
Store gluten-free egg muffins in the freezer in silicone cups (but not in a muffin tin) or between pieces of parchment paper so that they don’t stick together.
You can reheat them in the oven straight from the freezer. Heat them on low (275 degrees Fahrenheit) until heated through.
Make sure to cook the egg muffins at a lower temperature (300 degrees Fahrenheit), which helps prevent the rise and fall of egg muffins. Another trick is to use a bit of flour in the recipe, though it will void any paleo or Whole30 dietary needs.

More Whole30 Recipes You'll Love
If you tried this Gluten-Free Egg Muffins Recipe or any other recipe on my blog, please leave a 🌟 star rating and let me know how it goes!

Gluten-Free Egg Muffin Cups
Video
Equipment
Ingredients
- 6 eggs
- 1 cup egg whites
- 2 teaspoon garlic powder
- 1 teaspoon turmeric
- ½ teaspoon sea salt
- 2 tablespoons nutritional yeast
- ¼ cup almond milk
- ¼ teaspoon baking powder
- 1 cup broccoli finely chopped
- ½ cup spinach chopped
Instructions
- Preheat the oven to 300 degrees Farenheit.
- In a large bowl crack the eggs and whisk in the egg whites.
- Add in the seasonings and baking powder and mix well.
- Stir in the almond milk.
- If you haven't already, chop the broccoli and spinach and whisk into the bowl until coated.
- Prep 12 muffins tins with either non-stick spray or silicone muffin cups in a mufifn tin.
- Portion the batter into each cup making sure to get an even ration of veggies and eggs.
- Bake in the oven for twenty minutes then rotate the pan.
- Bake another 18-20 minutes until cooked through.
- Remove from the oven and let the egg muffins cool completely in the pan before removing them.
Notes
Disclaimer:
Nutrition values are estimates only, using online calculators. Please verify using your own data"










claudia says
I've never tried nutritional yeast in anything except on my popcorn, so this was a fantastic surprise! I added some red pepper too it was a great breakfast treat for my busy weekend.
fitasamamabear says
I do love it on popcorn too, ah the red pepper would be wonderful!
Jane says
These are so easy to make, and they're delicious! I made these for the first time the other night and my husband and I loved them.
fitasamamabear says
Ohh always a hit when hubby approves!
Sarah says
these are so great and so easy for school mornings..i loved the addition of tumeric which really set them apart from other egg muffins ive made.
fitasamamabear says
It's a nice little flavor switch!
Gina says
Love the finely chopped veggies in these! Such a great protein packed breakfast and easy to take on the go. Planning to make a batch every Sunday for easy weekday meal prep.
fitasamamabear says
It makes busy weeks a little more simple!
Mandy Applegate says
I made these for my nieces who visited at the weekend, apparently, they don't like veggies, even though they devoted a whole batch of these muffins that were stuffed...with veggies!
fitasamamabear says
Haha best feeling ever!
Carol Little R.H. @studiobotanica says
So love making 'egg muffins' like these. These invite such creativity -- you just know I add bitter greens into mine!
TASTY!!!
fitasamamabear says
Haha I am so jealous of your ability to add bitter greens to everything! You rock.
theresa says
I love grab-&-go options like this
fitasamamabear says
They keep life simple and sane!
Daniela says
These look delicious! I can absolutely get on board with these and love sneaking the extra veg in there. Win!
fitasamamabear says
Egg muffins are one of my favorites! So much healthy in one little cup.
Michelle Carnes says
These look awesome! I love sneaking veggies into everything, we'll definitely be trying these.
fitasamamabear says
We are all about the sneaking haha My daughters loved these though so I hope your kids do too!
!
GiGi Eats says
I really like the addition of nutritional yeast! Never thought about that for a recipe like this but it sounds genius to me! I am going to try these with unsweetened coconut milk!
fitasamamabear says
I sneak nutritional yeast into random things a lot haha gives it a little boost so yay! mmm they would b a bit creamier with coconut milk- nice swap!