These protein muffins combine a classic easy muffin recipe with simple swaps to boost the protein, giving you a light and fluffy muffin that leaves you satisfied.

I love muffins for an easy breakfast.
Ever since the kids were little, choosing Peanut Butter Chocolate Chip Muffins or Banana Bread Muffins or Pumpkin Chocolate Chip Muffins was pretty much a given as one of our breakfast options.
But kids who are now teenagers running track, plus a mom working on her own nutrition goals, mean those muffins need a little something extra.
So now, we’re all enjoying protein muffins!
HEALTHY PROTEIN MUFFINS
Let’s talk about why you want to add these protein muffins to your next meal prep.
- Protein. The default protein breakfast options might be eggs and meat, but making muffins high protein means enjoying yummy baked goods AND hitting the protein goals.
- Frugal. The highest-cost ingredient will be the protein powder, but because it’s spread out over the whole batch, and we’re choosing other frugal protein sources like Greek yogurt, these still fall on the lower end of cost compared to store-bought protein cookies or other packaged options.
- Perfect texture. Light and fluffy with plenty of moisture, these protein muffins turn out amazing every time.
- Freezer-friendly. Go ahead and double the batch for an easy option to pull from the freezer.
- Customizable. Stick with strawberry or switch it up with different mix-ins. See below for flavor options.
- Delicious! The most important part! My son didn’t even realize they were specifically protein muffins and went back for seconds…and thirds….

HIGH PROTEIN MUFFINS RECIPE INGREDIENTS
You’ll find pretty standard muffin ingredients here, with a few tweaks to boost the protein in muffins.
- Eggs. A couple of eggs help hold everything together and keep the muffins light and fluffy. I don’t recommend subbing flax egg here simply because you need the texture from the eggs.
- Unsweetened Applesauce. Applesauce adds moisture and natural sweetness. A mashed banana would also work if you prefer banana protein muffins.
- Coconut Oil. We’re using melted coconut oil for the fat here. Melted butter would probably work too.
- Greek Yogurt. Greek yogurt adds moisture and tang while boosting the protein in muffins. I used vanilla Oikos, but plain Greek yogurt would work too.
- Unsweetened Almond Milk. A little bit of almond milk keeps the protein muffins from turning out dry and crumbly.
- All-Purpose Flour. All-purpose white flour is the base for the high protein muffins.
- Protein Powder. A big part of what makes these muffins high protein. I like Legion French Vanilla. You can use a natural whey protein powder or a plant-based protein powder.
- Baking Powder + Baking Soda. Using both baking powder and baking soda gives you light, tender muffins with a good rise.
- Granulated Sugar. Just a little bit of sweetener takes these muffins from just okay to teen-approved!
- Salt. A bit of salt in baked goods helps bring out the sweetness.
- Fruit. Diced strawberries are my favorite, but blueberries or chopped peaches would be yummy too! (You could also make protein chocolate chip muffins by folding in chocolate chips instead of fruit.)

HOW TO MAKE HIGH PROTEIN MUFFINS RECIPE
Step 1. Preheat the oven to 375F. Spray a muffin tin with nonstick cooking spray or line with paper liners or silicone muffin cups.

Step 2. In a large bowl, combine the wet ingredients: eggs, applesauce, coconut oil, Greek yogurt, and almond milk. Whisk well.

Step 3. Add the dry ingredients: flour, protein powder, baking powder, baking soda, sugar, and salt. Use a spatula to gently combine the mixture.
The batter will be thick but should not be dry. If it looks dry, add additional almond milk 1 Tablespoon at a time, up to 2 Tablespoons.

Step 4. Gently fold in the chopped fruit.

Step 5. Scoop into the prepared muffin pan and bake for 15-17 minutes, until golden brown on top and a toothpick inserted into the center of a muffin comes out clean.
Store protein muffins in an airtight container at room temperature for up to 3 days or refrigerate for up to 1 week. If your house is anything like mine, they’ll be long gone before then! You can also freeze high protein muffins for up to 3 months.

PROTIEN MUFFINS TIPS
Make sure to drain any extra liquid from your fruit and chop it into small pieces. Large chunks might prevent the muffins from baking evenly, and you’ll end up with bits of raw batter near the fruit. Thaw frozen fruit before chopping it and adding it to the protein muffins.
Using protein powder in muffins means the tops of the muffins tend to brown quickly. Double-check with a toothpick inserted into the center of the muffin to make sure they are baked all the way through.
I used vanilla protein powder and vanilla yogurt for flavor and sweetness. If you choose plain options, add 1 teaspoon of vanilla extract for that same vanilla flavor.
BANANA PROTEIN MUFFINS AND OTHER VARIATIONS
From fresh blueberries to ripe bananas, make the protein muffins your own!
| Flavor | Adjustments | Result |
| Banana Protein Muffins | Swap 1 large mashed banana for applesauce | Slightly heavier, naturally sweet |
| Protein Muffins Pumpkin | Swap ⅓ cup pumpkin puree for applesauce and add 1 teaspoon of cinnamon | Soft and moist |
| Chocolate Protein Muffins | Reduce all-purpose flour to 1 ¾ cups, add ½ cup cocoa powder and 2 Tbsp additional sugar. Will likely need the additional 2 Tbsp of almond milk | Rich chocolate flavor, slightly chewy |
| Chocolate Chip Protein Muffins | Fold in ½ cup of chocolate chips instead of fruit | Sweet and tender |
| Blueberry Lemon Muffins | Choose blueberries for the fruit and add the zest/juice of 1 medium lemon. | Light and fluffy, with bright and tangy flavor |
SERVE WITH PROTEIN BREAKFAST MUFFINS
Each serving of protein muffins contains about 14 grams of protein, which makes them higher in protein than other baked goods. They are perfect for a grab-and-go snack! To round out breakfast, enjoy a muffin with one of these:
- Copycat Starbucks Egg Bites
- The Best Scrambled Eggs
- Homemade Breakfast Sausage
- Homemade Protein Shakes

HOW TO INCLUDE PROTEIN IN MUFFINS
To include protein in muffins or other baked goods, we’re making some simple swaps.
- Using Greek Yogurt for a larger portion of the wet ingredients keeps the muffins moist and also helps keep the total fat lower, all while adding 17g of protein to the batch of muffins!
- Swapping some of the flour for protein powder helps lower the carbohydrates slightly and adds a big boost of protein – my favorite brand adds 22g of protein. Depending on the brand you use, that amount might vary slightly, but it will still bump your total protein up by quite a bit.
Remember that the smaller amounts of protein in other ingredients like eggs and almond milk also add up. While they’re not specific protein boosters, the protein still counts.

PROTEIN POWDER MUFFINS FAQS
Do healthy protein muffins taste good?
Yes! My son said he didn’t even think they were protein muffins at first, and between both kids, half the batch disappeared the first day! They taste just like a standard yummy muffin.
How do you keep protein muffins from turning out dry?
Protein powder can make baked goods dry, which is why we’re adding applesauce, coconut oil, and Greek yogurt to really bump up the moisture. If the muffin batter still seems dry, add a little bit of additional almond milk.
Can you make high protein muffins with cottage cheese instead of Greek yogurt?
Probably. I haven’t tried that substitution in this recipe, but you can often swap out Greek yogurt for cottage cheese for a similar texture, flavor, and protein count. Regular plain yogurt and sour cream also usually work as substitutions, although they won’t be as high in protein.
MORE HIGH PROTEIN RECIPES
- High Protein Oatmeal
- 25+ Cheap and Healthy High Protein Foods
- Protein Pancakes
- High Protein Trail Mix
- Protein Waffles
- Protein Banana Bread
High Protein Recipes on Repeat
Download the top 15+ recipes that are on repeat in my house, making it easy to feed my family AND meet my protein goals!Easy Protein Muffins with Fruit
These protein muffins combine a classic easy muffin recipe with simple swaps to boost the protein, giving you a light and fluffy muffin that leaves you satisfied.
- Prep Time: 10 minutes
- Cook Time: 15-17 minutes
- Total Time: 25-27 minutes
- Yield: 12 muffins 1x
- Category: Breakfast
- Method: Baking
- Cuisine: American
Ingredients
Wet Ingredients:
- 2 large eggs (100g)
- ⅓ cup unsweetened applesauce (80g)
- ¼ cup liquid coconut oil (56g)
- 1 cup fat-free Greek yogurt (I used vanilla Oikos) (240g)
- ¼ cup unsweetened almond milk (60g)
Dry Ingredients:
- 2 ¼ cups all-purpose flour (281g)
- ¼ cup protein powder (I like Legion French Vanilla) (30g)
- 1 ½ tsp baking powder (6g)
- ½ tsp baking soda (3g)
- ¼ cup granulated sugar (64g)
- ½ tsp salt (3g)
Fruit:
- 1 ½ cups diced strawberries (or blueberries or peaches) (250g)
Instructions
- Preheat the oven to 375F. Spray a muffin tin with nonstick cooking spray or line with paper liners or silicone muffin cups.
- In a large bowl, combine the wet ingredients: eggs, applesauce, coconut oil, Greek yogurt, and almond milk. Whisk well.
- Add the dry ingredients: flour, protein powder, baking powder, baking soda, sugar, and salt. Use a spatula to gently combine the mixture. The batter will be thick but should not be dry. If it looks dry, add additional almond milk 1 Tablespoon at a time, up to 2 Tablespoons.
- Gently fold in the chopped fruit.
- Scoop into the prepared muffin pan and bake for 15-17 minutes, until golden brown on top and a toothpick inserted into the center of a muffin comes out clean.
- Store protein muffins in an airtight container at room temperature for up to 3 days or refrigerate for up to 1 week. You can also freeze high protein muffins for up to 3 months.
Notes
- Make sure to drain any extra liquid from your fruit and chop it into small pieces. Large chunks might prevent the muffins from baking evenly, and you’ll end up with bits of raw batter near the fruit. Thaw frozen fruit before chopping it and adding it to the protein muffins.
- Using protein powder in muffins means the tops of the muffins tend to brown quickly. Double-check with a toothpick inserted into the center of the muffin to make sure they are baked all the way through.
- I used vanilla protein powder and vanilla yogurt for flavor and sweetness. If you choose plain options, add 1 teaspoon of vanilla extract for that same vanilla flavor.


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