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    Home » Recipes » Gluten-Free Dairy-Free Breakfast Recipes

    Gluten-Free Egg Muffins [Meal Prep Breakfast])

    Modified: Jun 3, 2025 · by Shelby Stover · This post may contain affiliate links · 20 Comments

    Jump to Recipe
    Pinterest image with text: multiple images of egg muffins including in process images of how to make the egg muffins
    Pinterest image with text: keto egg muffins in a line seated on spinach with eggs and spinach in white bowls
    Pinterest image with text: two images the top of whole30 egg muffins in a line and the bottom of spinach being whisked into eggs

    Savory and loaded with nutrients, these gluten-free egg muffins are the perfect make-ahead breakfast! They have an ever-so-slight cheesy flavor and are perfect for a grab-and-go meal out the door. Plus, with only 47 calories and totally low-carb, they're a great way to keep your nutrition in check.

    : dairy-free egg muffins in a line seated on spinach with eggs and spinach in white bowls.

    For busy mornings in which you don't have time to whip anything up, I've got you covered. These gluten-free egg muffins are a great way to sneak veggies into your diet while grabbing breakfast out the door.

    They're a meal prep breakfast recipe (just like carnivore casserole) that freezes well, and I use them the most with my kids so they have something healthy in the morning.

    Why You'll Love This Recipe

    Easy-to-make: All you need to do is whip everything up in a bowl, portion, and bake for these egg muffins to come together.

    Nutritious: This breakfast recipe fits into any dietary need. The egg muffins are dairy-free, gluten-free, keto, paleo, and Whole30 approved.

    Versatile: You can learn more below about the many ways you can vary the taste of the recipe.

    Ingredients You Need

    Most of the ingredients needed are basic kitchen staples or high protein food staples, and you already have them on hand.

    You want to use both eggs and egg whites as the whites have more protein in them. As for seasonings, you can adjust or eliminate them as you prefer. I use garlic, turmeric, salt, and pepper.

    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.

    Know that any vegetables will work for the recipe, but chop them finely so that they fully cook and don't create air pockets.

    Looking for a vegan option? Check out these vegan egg muffins.

    How To Make Gluten-Free Egg Muffins

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

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

    Almond milk being poured from a yellow measuring cup into a mixing bowl of eggs
    Spinach and a whisk in a bowl of raw scrambled eggs

    Step 3: Portion the egg mixture into a silicone muffin pan (or use liners) and baked until cooked through.

    healthy egg muffins with spinach in red silicone muffin cups in a muffin tray
    Portion into a muffin tin and bake.

    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.

    Cooking the gluten-free breakfast egg muffins in paper cups makes them hard to peel off when reheating.

    Chop the veggies very small so that there are no large chunks and everything cooks through (especially important if the muffins are for very young toddlers).

    Let them cool in the pan slowly so that they don’t deflate immediately out of the oven.

    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.

    dairy-free egg muffins in a line seated on spinach with eggs and spinach in white bowls

    Variations

    Below are a few ways we vary the flavor of the egg cups as to what we want that week. More often than not, I add in more protein!

    • Skip the broccoli and add in chopped bell peppers or cauliflower.
    • Opt to add sliced leek in place of spinach.
    • Add some chopped bacon or gluten-free sausage into the egg mixture for additional protein and savory flavor!

    Frequently Asked Questions About Whole30 Egg Muffins

    How do you meal prep egg muffins?

    You want to cook the egg muffins fully before storing them. Once cooled, store them in the freezer or fridge in their silicone molds in an airtight container.

    How do you store the egg muffins for meal prep?

    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.

    How do you reheat egg muffins?

    You can reheat them in the oven straight from the freezer. Health them on low (275 degrees Fahrenheit) until heated through.

    Why do my egg muffins go flat?

    Make sure to cook the whole30 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 the whole30 approval.

    Other Whole30 Recipes

    • Spicy whole30 deviled eggs
    • Whole30 whipped cream
    • Sheet pan sausage and veggies
    • Chocolate cherry smoothie
    • Gut healing smoothie
    • Tuna stuffed avocados
    • Anti-inflammatory smoothie recipe
    • Best cauliflower rice
    • Green avocado smoothie bowl
    • Whole30 ice cream

    dairy-free egg muffins in a line seated on spinach with eggs and spinach in white bowls

    Dairy-free egg muffins in a line seated on spinach with eggs and spinach in white bowls.

    Gluten-Free Keto Egg Muffins

    Shelby Stover
    Savory in flavor and packed with nutrients these gluten-free egg muffins are a tasty, keto meal prep recipe for busy days.
    5 from 5 votes
    Print Recipe Pin Recipe
    Prep Time 5 minutes mins
    Cook Time 40 minutes mins
    10 minutes mins
    Total Time 55 minutes mins
    Course Breakfast
    Cuisine American
    Servings 12 muffins
    Calories 53 kcal

    Video

    Equipment

    • Silicone muffin cups

    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

    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.
    Cooking the gluten-free breakfast egg muffins in paper cups makes them hard to peel off when reheating.
    Chop the veggies very small so that there are no large chunks and everything cooks through (especially important if the muffins are for very young toddlers).
    Let them cool in the pan slowly so that they don’t deflate immediately out of the oven.
    Nutrition is broken down per egg muffin. Eat multiple muffins for a protein-based breakfast or add in some chopped chicken or ground beef.
    To reheat the muffins, place them in the oven directly from the freezer at 250 degrees Fahrenheit. Heat until cooked through (about 15 minutes). Heating them too quickly will deflate them.
    Disclaimer:

    Nutrition values are estimates only, using online calculators. Please verify using your own data"

    Nutrition

    Calories: 53kcalCarbohydrates: 2gProtein: 6gFat: 2gSaturated Fat: 1gPolyunsaturated Fat: 0.5gMonounsaturated Fat: 1gTrans Fat: 0.01gCholesterol: 82mgSodium: 172mgPotassium: 137mgFiber: 1gSugar: 0.4gVitamin A: 282IUVitamin C: 7mgCalcium: 29mgIron: 1mg
    Keyword dairy-free egg muffins, egg muffins, eggs, keto eggo muffins, whole30 breakfast recipe
    Have You Tried This Recipe?Please leave a star rating and comment below. Mention @fitasamamabear or tag #fitasamamabear!

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      Dairy-Free Egg Bites
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    • Wooden bowl with a coffee protein smoothie in it topped with granola, chocolate chips, bananas, and peanut butter.
      High Protein Coffee Smoothie Bowl [Dairy Free]

    Comments

    1. claudia says

      August 15, 2023 at 8:13 pm

      5 stars
      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.

      Reply
      • fitasamamabear says

        August 17, 2023 at 1:52 pm

        I do love it on popcorn too, ah the red pepper would be wonderful!

        Reply
    2. Jane says

      August 15, 2023 at 6:41 pm

      5 stars
      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.

      Reply
      • fitasamamabear says

        August 17, 2023 at 1:52 pm

        Ohh always a hit when hubby approves!

        Reply
    3. Sarah says

      August 15, 2023 at 5:24 pm

      5 stars
      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.

      Reply
      • fitasamamabear says

        August 17, 2023 at 1:51 pm

        It's a nice little flavor switch!

        Reply
    4. Gina says

      August 15, 2023 at 2:59 pm

      5 stars
      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.

      Reply
      • fitasamamabear says

        August 17, 2023 at 1:51 pm

        It makes busy weeks a little more simple!

        Reply
    5. Mandy Applegate says

      August 15, 2023 at 1:37 pm

      5 stars
      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!

      Reply
      • fitasamamabear says

        August 17, 2023 at 1:51 pm

        Haha best feeling ever!

        Reply
    6. Carol Little R.H. @studiobotanica says

      June 15, 2018 at 3:08 am

      So love making 'egg muffins' like these. These invite such creativity -- you just know I add bitter greens into mine!
      TASTY!!!

      Reply
      • fitasamamabear says

        June 16, 2018 at 5:57 pm

        Haha I am so jealous of your ability to add bitter greens to everything! You rock.

        Reply
    7. theresa says

      June 15, 2018 at 1:08 am

      I love grab-&-go options like this

      Reply
      • fitasamamabear says

        June 16, 2018 at 5:57 pm

        They keep life simple and sane!

        Reply
    8. Daniela says

      June 14, 2018 at 7:00 pm

      These look delicious! I can absolutely get on board with these and love sneaking the extra veg in there. Win!

      Reply
      • fitasamamabear says

        June 14, 2018 at 7:31 pm

        Egg muffins are one of my favorites! So much healthy in one little cup.

        Reply
    9. Michelle Carnes says

      June 14, 2018 at 5:22 pm

      These look awesome! I love sneaking veggies into everything, we'll definitely be trying these.

      Reply
      • fitasamamabear says

        June 14, 2018 at 7:31 pm

        We are all about the sneaking haha My daughters loved these though so I hope your kids do too!
        !

        Reply
    10. GiGi Eats says

      June 14, 2018 at 1:43 pm

      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!

      Reply
      • fitasamamabear says

        June 14, 2018 at 4:02 pm

        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!

        Reply
    5 from 5 votes

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    I'm Shelby, a Certified Strength & Nutrition Coach who has spent the last 10 years helping women feel more comfortable in their skin though home strength training and healthy food- no diets, no shortcuts

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