These protein muffins are soft, tender, and lightly sweet, with 10 grams of protein in each one. They have the texture of a classic muffin, without peanut butter, banana, or another strong flavor taking over.
They’re made with familiar ingredients and taste like muffins first, not protein food. Leave them plain or add mini chocolate chips.
Why this recipe works
I tested this recipe extensively to balance tenderness and structure. The result is muffins with a lightly sweet, tender crumb that’s not too moist to rise tall but never tastes dry.
A combination whey/casein protein powder adds plenty of protein without drying them out. Oat flour and eggs create a soft crumb with enough structure to rise and hold its shape as the muffins cool.
Applesauce adds moisture without bringing a strong flavor like banana, and Greek yogurt adds richness and just enough moisture. Brown sugar and a little oil, which is truly optional, help keep the crumb tender and fresh.
Recipe ingredients
Here’s what you need to make these muffins, plus a short explanation of the role of each ingredient in an ideal baked result. For full ingredient amounts, scroll down to the recipe card:
- Oat flour: Provides a traditional muffin crumb with a soft, tender texture and mild natural sweetness. The finer the oat flour, the softer the crumb. You can grind your own from rolled oats, but sift it well to remove any larger pieces.
- Protein powder: Adds protein and helps the muffins rise and set without becoming fragile. A whey-casein blend like PEScience gives the best balance of structure from the whey and moisture retention from the casein for a soft crumb. The best balance is about half whey, half casein.
- Baking powder & baking soda: Baking powder adds rise; baking soda reacts with the acidic Greek yogurt for a little extra lift and helps the muffins brown in the oven.
- Salt: Brightens the other flavors.
- Brown sugar: Adds sweetness and helps lock in moisture for a tender crumb.
- Greek yogurt: Provides concentrated moisture without thinning the batter and richness from its fat. Its tangy acidity adds flavor and activates the baking soda for extra lift.
- Applesauce: Provides moisture for the protein powder to absorb; its pectin and fruit solids help give the muffins structure and a soft, uniform crumb.
- Eggs: Add structure so the muffins rise and hold their shape as they cool, plus fat from the yolks for a softer texture and richer mouthfeel.
- Vanilla: Adds depth of flavor. I prefer vanilla bean paste for a richer flavor, but vanilla extract works well, too.
- Oil: Gives the muffins a softer, more tender crumb that tastes moist, and helps them stay fresh longer. Any neutral oil will work, like peanut, grapeseed, canola, vegetable, or avocado. You can leave it out, though, entirely.
- Mini chocolate Chips: Add flavor and texture, but you can leave them out. They also help the muffins bake a little taller by lowering the moisture ratio. Mini chips spread throughout the batter, so you get more chocolate in every bite. Try raisins or chopped pecans or walnuts instead.
How to make protein muffins (step by step photos):
This visual overview of how to make these muffins should help you imagine how to make them at home. I’ve also included the reasons behind each step:
Prepare the muffin tin
These muffins tend to stick to all paper liners, and even worse to bare muffin wells. Spray 12 greaseproof muffin liners lightly with cooking oil spray to help with release, then place them in the muffin tin.
Steps 1-2: Combine dry ingredients
In a large mixing bowl, whisk all the dry ingredients (oat flour, protein powder, baking powder and soda, salt) plus brown sugar fully so you don’t need to overwork the batter after adding the liquids. Break up the lumps in your brown sugar with the back of a mixing spoon to avoid hard lumps in your muffins.
Step 3: Add wet ingredients
Make a well in the center of the dry ingredients and add the applesauce, yogurt, beaten eggs, vanilla and optional oil. Turn over the batter carefully just until everything is combined. The batter is high in protein, so overmixing can make the muffins less tender as they bake.
Step 4: Let the batter rest
The batter will be relatively thin, which can make it harder for the muffins to rise tall. Letting the batter rest in the bowl for just a few minutes lets the dry ingredients absorb some moisture without mixing more for a thicker batter that rises higher.
Add the optional chips
Mix in the optional miniature chocolate chips just until combined, but reserve some to sprinkle on top of the batter so they’re visible after baking.
Step 5: Transfer batter
Divide the batter evenly among the wells of the muffin tin. In my muffin tin, the batter fills the wells more than 3/4 of the way full, but that will depend on the size of your wells. Sprinkle any remaining mini chips evenly over the tops of the batter in the wells.
Step 6: Bake
Bake at 350°F for 5 minutes to help boost the muffins into a tall rise, then reduce the oven temperature to 325°F for another 10 minutes to give them time to set without drying out. When they’re done, the muffins will mostly feel firm on top, but be careful not to overbake them. Remove them from the pan as soon as possible to stop the baking and let them cool on a wire rack.
Expert tips
Grease the muffin liners
Because these muffins have so much moisture, they tend to stick to even the best cupcake tin liners. Through lots of recipe testing, I learned that reducing the moisture enough to prevent sticking made the muffins taste dry. Instead, I recommend greasing the paper liners with cooking oil spray lightly before filling them to get them to release after cooling.
Don’t overbake
Since all protein powders absorbs a lot of moisture in baking, it’s important to err on the side of underbaking rather than overbaking these muffins. If you underbake them slightly, the very tops of the domes will collapse a little as they cool but the muffins won’t be raw at all. If you overbake, the whole muffin may taste dry.
Ingredient substitutions
If you use oats marked gluten free and source your other ingredients carefully, these muffins are naturally gluten free. If you need to avoid other allergens, here are my suggestions:
Dairy free
In place of the yogurt, try your favorite plain nondairy yogurt, strained of enough moisture to have the texture of Greek-style yogurt. The more difficult replacement is the protein powder, since this recipe was developed for a combination casein and whey protein powder which helps the muffins hold their shape but prevents them from drying out. If you use a vegan protein powder, I’d try using 45 to 50 grams of the powder instead of the 62 called for in the recipe, and increasing the applesauce by an extra 20 grams.
Egg free
In place of the 2 eggs, you can try using 2 “flax eggs” or “chia eggs,” Bob’s Red Mill egg replacer, or JustEgg liquid egg replacer in the refrigerated section. You can also try replacing them with 80 grams more plain Greek-style yogurt and 20 grams more oat flour.
Oat free
In place of oat flour, try grinding quinoa flakes into a powder and sifting out any remaining larger pieces. Be sure to measure by weight, not volume, since quinoa flakes are very light.
No applesauce
If you can’t have applesauce, try replacing it with an equal amount, by weight, of very ripe mashed bananas. The muffins will taste like banana, though.
Storage instructions
These muffins are best the first day they’re baked, but you can store them at room temperature in a sealed container for up to 2 days. Adding oil helps keep them from drying out on day 2. For longer storage, wrap each tightly in freezer-safe wrap and freeze for up to 3 months. Defrost at room temperature or for 20 seconds in the microwave.
Protein Muffins Recipe with protein powder
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Ingredients
- 1 ¾ cups finely ground and sifted oat flour (gluten free if necessary)
- 2 scoops casein-whey protein powder (See Recipe Notes)
- 1 ½ teaspoons baking powder
- ½ teaspoon baking soda
- ½ teaspoon kosher salt
- ⅔ cup packed light brown sugar
- ¾ cup smooth applesauce at room temperature
- ¾ cup lowfat plain Greek-style yogurt at room temperature (avoid nonfat; whole milk is fine)
- 2 eggs at room temperature, beaten
- 1 teaspoon vanilla bean paste or vanilla extract
- 2 tablespoons neutral oil optional (See Recipe Notes)
- ⅔ cup mini chocolate chips optional
Instructions
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Preheat oven to 350°F. Line a 12-cup muffin tin with liners and spray the liners lightly with oil.
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In a large mixing bowl, whisk together oat flour, protein powder, baking powder, baking soda, salt and brown sugar. Break up any lumps in the brown sugar with the back of a spoon.
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Create a well in the center of the dry ingredients and add applesauce, yogurt, eggs, vanilla and optional oil.
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Mix with a spoon or spatula just until combined. The batter will be relatively thin and soft.
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Let the batter rest in the mixing bowl at room temperature for 10 minutes to thicken.
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Mix in most of the optional chocolate chips, reserving about 2 tablespoons to sprinkle on top.
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Divide the batter evenly among 12 muffin wells. The wells should be nearly full, but that will depend on the size of each muffin well and whether you’ve added the chips.
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Sprinkle any reserved optional mini chocolate chips evenly on the top of the batter in each well. Tap the pan a few times on the counter to break any large bubbles and help the chips adhere.
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Bake in the center of the preheated oven for 5 minutes. Reduce the oven temperature to 325°F and bake about 10 minutes more. The muffins are done when the tops are mostly firm to the touch and not shiny. The very tops of some of the domes may seem too soft to hold, but it’s important not to overbake or the muffins may dry out.
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Transfer to a wire rack as quickly as possible to stop baking. Let the muffins cool completely before peeling the liners.
Notes
For the best texture, use a whey-casein blend, ideally about half whey and half casein, such as PEScience.
Oil
Optional, but it makes the muffins taste more tender and helps keep them from drying out on the second day. You can use any neutral oil, like grapeseed, canola, avocado, peanut, or vegetable.
Muffin liners
These muffins tend to stick, so lightly spray even greaseproof liners with cooking oil and let the muffins cool completely before peeling them.
Approximate nutritional information includes mini chocolate chips and oil.
Nutrition
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