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Apple Cinnamon Protein Muffins

These freshly-baked apple cinnamon muffins are sweetened with honey and packed with vanilla protein for a quick, easy breakfast. Their warm spice and moist tenderness won’t let you skip the most important meal of the day even if you’re in a rush!

A stack of apple cinnamon protein muffins.

Easy Apple Cinnamon Muffins

If you’re in the market for an effortless breakfast recipe, these spiced apple cinnamon muffins are for you. Lots of vanilla protein powder makes them super hearty but also adds sweetness. To prevent any sugar highs, there are no processed sugars in the batter— only raw honey. Baked until light and fluffy, the sprinkle of cinnamon, earthy nutmeg, and cardamom add the perfect amount of coziness. Whether you make one or more batches, you’ll always keep them in the fridge or freezer from now on for a sweet bite in the morning.

Why You’ll Love These Apple Muffins

You’ll no longer skip breakfast after you see how easy to make these fluffy apple muffins are.

  • Wholesome. They’re packed with Greek yogurt, protein powder, and plant-based flours to fuel your mornings.
  • Great for meal prep. Keep them in the fridge or freezer and pop them out whenever you need a quick breakfast.
  • Dessert for breakfast. These muffins are warmly spiced and full of tender apples, just like your favorite bakery treats, but they’re actually okay for breakfast.
  • Easy. Stir the batter, pour it into the muffin pan, and bake away.
A bitten-into apple muffin with the muffin tray in the background.

What You’ll Need

The best apple muffins must have honey and cinnamon in them. I’ve added plenty! Scroll to the recipe card at the bottom of the post for exact measurements.

  • Oatmeal flour – Make it yourself by processing gluten-free old-fashioned oats until the mixture is super fine.
  • Almond flour You can find this in the organic or baking aisles in most grocery stores.
  • Vanilla whey protein powder Vegan protein powder is a good swap.
  • Cinnamon – If you only have cinnamon sticks, throw them into the food processor until you get a fine powder.
  • Nutmeg Skip it if you’ve run out but don’t swap it for more cinnamon.
  • Cardamom It needs to be ground cardamom.
  • Baking powder Check the expiration date before adding it in.
  • Baking soda Don’t swap it for baking powder because the muffins will have a metallic after-taste.
  • Salt Kosher salt is best.
  • Egg whites Liquid egg whites work too.
  • Non-fat Greek yogurt – Regular Greek yogurt is okay as well.
  • Unsweetened applesauce – If it’s sweetened, reduce the amount of honey in the recipe.
  • Honey Feel free to use maple syrup or agave nectar.
  • Vanilla extract You can use almond extract instead or leave it out completely.
  • Apple I prefer Honeycrisp, Gala, or Pink Lady.
A stack of three apple muffins.

How to Make Apple Cinnamon Muffins

These apple cinnamon muffins are as easy as your favorite box mix. Scroll to the recipe card at the bottom of the post for more detailed instructions.

  • Prep the oven. Preheat the oven to 350F. Line a muffin pan with muffin liners. Set it aside.
  • Mix the wet ingredients. Combine the egg whites, yogurt, applesauce, honey, vanilla extract, and apples in a large bowl until smooth.
  • Combine the dry ingredients. Whisk the oatmeal flour, almond flour, protein powder, cinnamon, nutmeg, cardamom, baking powder, baking soda, and salt in a separate bowl.
  • Bring them together. Gradually combine the dry and wet ingredients, stirring until a smooth batter forms. It’s okay if a few small lumps remain.
  • Pour the batter. Fill each muffin liner until about ¾ of the way full. Don’t add more than this or they’ll over-flow in the oven.
  • Bake. Pop the muffin pan into the oven for 20 minutes or until a toothpick inserted in the center comes out clean.

Tips & Variation Ideas

Add some buttery streusel on top of your apple cinnamon muffins for a bakery-style treat.

  • Make them chocolatey. Use chocolate protein powder instead of vanilla and add 1/4 cup mini chocolate chips into the batter.
  • Add a streusel topping. Mix 1/2 cup old-fashioned oats, 3-4 tablespoons brown sugar, 1/4 teaspoon ground cinnamon, and 3 tablespoons melted butter. Sprinkle the mixture on top of the batter before baking. Remove the muffins from the oven when the streusel is golden and crispy.
  • Use more add-ins. Stir 1/4-1/2 cup dried cranberries or chopped pecans into the batter for more flavor.
  • Frost them. Use your favorite salted caramel, cream cheese, or cinnamon frosting to decorate the muffins and add some creamy goodness.
  • Add a filling. Once baked and cooled, scoop out about 2 teaspoons from the center of the muffin. Fill the cavity with apple pie filling or almond butter. Top with frosting and enjoy.
  • Toss the apples. Mix the diced apples with 1 tablespoon flour until completely coated. Add them into the batter as usual. This will prevent the apples from sinking to the bottom.
Bitten-into muffin.

How to Store Apple Muffins

Throw them into your bag straight out of the fridge or freezer for a last-minute breakfast.

  • Counter: Place them in an airtight container away from direct heat and sunlight for up to 5 days.
  • Fridge: Pop them into an airtight container or Ziploc bags for up to 9 days. Set them on the counter for 5-10 minutes before serving so they come down to room temperature.
  • Freezer: Wrap each cooled muffin in plastic wrap twice. Transfer them to a freezer-friendly bag or container. Freeze for up to 3 months. Thaw them overnight in the fridge or on the counter for 30 minutes.

More Muffin Recipes to Try

A stack of apple cinnamon protein muffins.

Apple Cinnamon Protein Muffins

5 from 2 votes
This quick apple cinnamon muffins recipe is an excuse to have dessert for breakfast while loading up on protein.
Prep Time10 minutes
Cook Time20 minutes
Total Time30 minutes
Servings: 12 muffins


  • 1 cup oatmeal flour old-fashioned gluten-free oats ground in food processor
  • ¼ cup almond flour
  • 3 scoops Vanilla Whey Protein Powder
  • 3 teaspoon cinnamon
  • 1/4 teaspoon nutmeg
  • 1/4 teaspoon cardamom
  • teaspoon baking powder
  • ½ teaspoon baking soda
  • 1/4 teaspoon salt
  • 3 egg whites
  • ½ cup nonfat Greek Yogurt
  • 1 cup unsweetened applesauce
  • 1/4 cup honey
  • 1 teaspoon vanilla extract
  • 1 cup medium-size apple cored and finely chopped


  • Preheat oven to 350°.
  • Place liners in one muffin pan and lightly spray with organic baking spray.
  • In a large bowl combine egg whites, yogurt, applesauce, honey, vanilla extract and apple pieces.
  • In a second bowl combine oatmeal flour, almond meal, vanilla whey protein powder, cinnamon, nutmeg, cardamom, baking powder, baking soda, and salt.
  • Combine flour mix and egg mix together until smooth.
  • Fill each tin ¾ of the way full, spreading evenly.
  • Bake for 20 minutes.
Course: Breakfast, Breakfast/Brunch, Dessert
Cuisine: American


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6 comments on “Apple Cinnamon Protein Muffins”

  1. Can you please let me know how many grams in total you used for the protein powder? Scoop sizes vary greatly! Thanks!

  2. 5 stars
    Hi Amy, this is a very cool recipe. Breakfast is the most important in my daily routine and having muffins with protein is the way to go. You know that most muffins are sweet and fatty but these ones are very cool. Didn’t you try to use Strawberry instead of Vanilla Whey Protein Powder? Thanks.

  3. Hi I’m wondering what is the purpose of the applesauce? I’d love to make these but applesauce makes me gag haha. Thanks!

    1. Isabela, it is acting as a binder and adding moisture in this recipe. With the fresh apples it is also great for adding flavor. You could use a stick of butter, and 2 whole eggs {remove egg whites from recipe}. Hope this helps.

  4. Avatar photo
    Mariana Sarceda

    5 stars
    Mmm!! Delicious and healthy! I love apples in every way possible. What a delicious way of using them!

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