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Protein Muffins

5 from 54 votes

You will instantly fall in love with this delicious recipe for soft, fluffy, and secretly healthy protein muffins!

Healthy High Protein Muffins

The best protein muffins

If you’re looking for a nutritious breakfast or healthy snack, be sure to give this super easy protein muffin recipe a try.

The muffins are just 100 calories, with over 10 GRAMS of protein each!

One pillow soft bite, and it’s almost impossible to believe the stellar nutrition facts. They taste like real bakery style muffins yet are secretly healthy at the same time.

The recipe can be whole grain, vegan, gluten free, added sugar free, egg free, oil free, low fat, and low calorie, with no banana required.

Also make these Healthy Blueberry Muffins

The Best Vegan Protein Muffins

High Protein Muffin Flavors

Chocolate Protein Muffins: Use your favorite chocolate protein powder. For double chocolate muffins, add a handful of regular or mini chocolate chips.

Protein Pumpkin Muffins: Instead of yogurt, use canned pumpkin puree. Increase cinnamon to two teaspoons and add a half teaspoon of pumpkin pie spice as well.

Nutella Protein Muffins: Swap the oil for this Homemade Nutella Recipe or for store bought chocolate hazelnut butter. Stir in a fourth cup of finely chopped hazelnuts.

Blueberry Protein Muffins: Use blueberry flavored yogurt, and place a few blueberries into each muffin top just before baking. This same method can be used to make raspberry, blackberry, cherry, or strawberry muffins.

High Protein Lemon Muffins: Go with a lemon flavored yogurt, and stir the zest of one lemon into the batter when you add the liquid ingredients.

Chocolate Chip Protein Muffin Ingredients

Healthy protein muffin ingredients

You will need flour, protein powder, sugar or granulated sweetener, ground cinnamon, baking powder, baking soda, salt, yogurt, water, pure vanilla extract, white or apple cider vinegar, optional egg whites, and optional oil or nut butter.

Types of flour that work include oat flour, white flour, some brands of gluten free all purpose flour, and spelt flour (my personal favorite).

We cannot vouch for whole wheat flour, pastry flour, chickpea flour, almond flour, or coconut flour. If you are looking for low carb muffins, try these Keto Muffins.

Pretty much any all purpose granulated sweetener will do well, including regular sugar, brown sugar, coconut sugar, or date sugar. We have not tried a liquid sweetener like honey or pure maple syrup. Be sure to report back with results if you try.

For protein muffins with no sugar added, use xylitol or granulated erythritol.

Step by step recipe video

Watch the protein muffin recipe video above

Protein Mini Muffins

Vegan protein muffins

For dairy free protein muffins with no eggs, simply increase the water to half a cup instead of adding egg whites.

You can use a non dairy yogurt, such as coconutmilk yogurt or soy yogurt.

Or replace the yogurt with an equal amount of pumpkin or sweet potato puree, unsweetened applesauce, or mashed banana. Only if using mashed banana, it is fine to decrease the sugar in the recipe to a third cup.

Vegan guests will also love these Vegan Brownies or Vegan Chocolate Chip Cookies.

Baking Homemade Protein Muffins In The Oven

How to make protein muffins

Gather all ingredients, and preheat the oven to 350 degrees Fahrenheit.

Line each cup of a muffin tin with cupcake liners, or grease the cups with oil spray.

In a large mixing bowl, whisk together the yogurt, water, pure vanilla extract, vinegar, and optional eggs and oil or nut butter.

To save time, you can combine the dry ingredients weeks, or even months, in advance if you wish. Store this homemade protein muffin mix in a large sealed Ziploc bag or container until ready to use.

Stir the flour, protein powder, dry sweetener, cinnamon, baking soda, salt, and baking powder into the mixing bowl. If adding chocolate chips, mix them in here as well.

Only stir until just evenly mixed. This will prevent the muffins from becoming tough, dense, and overly chewy once baked.

Scoop muffin batter into the prepared cups, dividing the batter evenly among the cups. It should fill around two thirds of each lined cup.

Bake the muffin pan on the oven’s center rack for nineteen minutes. Check for doneness by inserting a toothpick into the center of a muffin. If they are done, it should come out mostly clean.

Allow the pan to cool for ten minutes or so. Then remove the muffins.

What protein powder to use?

Use a brand and flavor of protein powder that you know you like.

I recommend unsweetened protein powder when baking, because it allows you to control the sweetness of recipes and avoid an artificial aftertaste.

However, feel free to experiment with other flavors, such as birthday cake batter, vanilla, caramel, coffee, or cookies and cream.

I often choose unflavored pea protein powder for these muffins. They will work with other forms of protein as well.

Grocery stores and health food stores should sell numerous types of protein powders, including whey protein, soy protein, brown rice, egg, hemp, casein, collagen, and pumpkin seed protein.

How To Store Homemade Muffins

Making protein mini muffins

If you prefer mini muffins to larger ones, grease or line a mini muffin pan.

Decrease the baking time to just twelve minutes.

This protein muffin recipe will yield around 20-22 mini protein muffins of a similar size to the ones in the video and photos here.

Recipe storage tips

I’ve found that if you let the muffins sit on the counter or in the refrigerator, loosely covered with cloth or paper towels, the liners peel off easily by the next day.

This works for the version with no oil as well.

After a day, store leftover protein muffins in an airtight container in the refrigerator for up to five days. Or freeze the muffins for up to three months.

If you’d like to reheat leftover muffins, first slice them in half and add butter, honey, agave, or a spread of choice. Toast in a regular or toaster oven.

Gram measurements for protein muffins

If you prefer to bake with a food scale instead of the cups and measuring spoons listed further below, here are the amounts to measure:

60 grams flour, 60 grams protein powder, 100 grams dry sweetener, 120 grams yogurt, 60 grams water, 60 grams egg or additional water, 36 grams oil or additional water, and 12 grams pure vanilla extract.

(If omitting the egg whites and oil, you will simply use 156 grams of water.)

Also be sure to include the baking powder, baking soda, salt, and cinnamon.

Healthy Vegan Muffins Recipe

Other healthy muffins

Banana Muffins

Bran Muffins

Applesauce Muffins

Healthy Muffins (15 flavors)

Peanut Butter Muffins

Healthy Mini Muffins With Protein Powder
Pin it now to save for laterPin Recipe

Protein Muffins

These soft and fluffy healthy protein muffins are a nutritious breakfast or snack recipe.
Cook Time 19 minutes
Total Time 19 minutes
Yield 9 muffins
5 from 54 votes


  • 1/2 cup yogurt (use nondairy for vegan)
  • 1/4 cup water
  • 1/4 cup egg whites or additional water
  • 3 tbsp oil, nut butter, or additional water
  • 1 tsp pure vanilla extract
  • 2 1/2 tsp white or cider vinegar
  • 2/3 cup flour
  • 1/2 cup protein powder
  • 1/2 cup sugar, unrefined or xylitol if desired
  • 1/2 tsp cinnamon
  • 1/2 tsp each: baking powder, baking soda, and salt
  • optional chocolate chips


  • Preheat the oven to 350 F. Grease or line a muffin tin. Whisk the wet ingredients in a bowl. Stir in remaining ingredients just until evenly mixed. Pour into the muffin tins. Bake 19 minutes. The protein muffins should look domed when you take them out. Allow to cool before removing from the tins. If you let them sit loosely covered overnight, the liners peel off easily by the next day.
    *If you prefer to make mini muffins like the ones in the photos and recipe video, decrease baking time to 12 minutes. It will yield 22 mini muffins.
    View Nutrition Facts


Readers also love this Protein Banana Bread.

Have you made this recipe?

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Published on August 6, 2023

Meet Katie

Chocolate Covered Katie is one of the top 25 food websites in America, and Katie has been 
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ABC's 5 O’Clock News. Her favorite food is chocolate, and she believes in eating dessert every single day.

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  1. Jillian says

    5 stars
    Hi Katie, I am a big fan of your recipes! Hope to make this one with blueberries tomorrow. Would it be very hard to add a “Jump to Recipe” feature at the top? I always read, but when pulling up the recipe on Pinterest it would be nice to avoid the scroll down. Not a big deal though if too much. Thanks

    • CCK Media Team says

      It’s not something we know how to do but is on the list for the next time Katie’s blog goes through a redesign 🙂

  2. Charlotte says

    Hi, these seem to be mini muffins, are there any reasons not to make them full-sized? Recommendations on modifications for cooking, etc if doing larger muffins? Thanks

    • CCK Media Team says

      Sorry for the confusion, the recipe is for full size, large muffins. If you’d like to make mini muffins like Katie did for the video and photos, decrease the baking time to 12 minutes and it will yield 22-24 mini muffins. We will edit the post today to make this more clear!

  3. Megan Newlan says

    How did you calculate fat grams? 3 tablespoons of oil divided by 9 muffins equals about 5 grams of fat per muffin, not 0.4 grams. The calorie count for the fat alone is 45 calories. 10 grams of protein is another 40 calories. 8 grams of carbs is 32 calories. That adds up to 117 calories per muffin for the no sugar added recipe.

    • CCK Media Team says

      Oil is optional in the recipe and therefore not included in nutrition facts, as is the standard when calculating nutrition facts with more than one ingredient option. You can easily make them without oil.

  4. Krista Dykes - says

    5 stars
    I just made these so my husband and I have a quick post-workout breakfast option. They’re PERFECT and so delicious. Will definitely be making them again. So happy these are protein packed too. Thanks Katie!!

5 from 54 votes (47 ratings without comment)

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