Protein Blueberry Muffins with Brown Sugar Topping

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These protein blueberry muffins are easy to make and extremely satisfying. We use all-purpose flour for that classic muffin taste & texture… protein to balance the macros… and reduced fat to save some calories. You can sneak these into a bake sale and no one will ever guess they’re a “healthy” version.

these protein blueberry muffins are moist and flavorful

So grab a large bowl because we’re gonna make high protein blueberry muffins without sacrificing any of their delicious taste or texture. This easy-to-make recipe makes 12 large muffins that are perfect if you’re craving a quick bite at home or preparing for a picnic at the park.

How To Make Protein Blueberry Muffins

For the best protein muffins, you need to put a little extra care and attention into them, but I promise you, it’ll be worth it. Follow the recipe below and reference the video if you want to see all the steps in action. And for more in depth information on each ingredient, substitutions, variations, expert tips, and more, reference the full post after the recipe card.

Important Notice About Measurements

While every effort has been made to make sure the US / volumetric measurements are generally accurate, We do not recommend using them. There is no guarantee your specific ingredients or your specific scooping technique will measure the same as ours. For the best results, especially with baking recipes such as this one, use a food scale and measure by weight.

Blueberry Muffins with Brown Sugar Topping

These protein blueberry muffins are easy to make and extremely satisfying. We use all-purpose flour for that classic muffin taste & texture… protein to balance the macros… and reduced fat to save some calories. You can sneak these into a bake sale and no one will ever guess they’re a “healthy” version.
Prep Time 15 minutes
Cook Time 20 minutes
Total Time 35 minutes
Course Breakfast, Dessert
Servings 12 muffins
Calories 147 kcal


Dry Ingredients

  • 225 g blueberries fresh, washed
  • 120 g all-purpose flour
  • 60 g unflavored whey protein
  • 60 g collagen peptides
  • 60 g soluble corn fiber
  • 7.8 g xanthan gum
  • 6 g salt
  • 9.6 g baking powder
  • 3 g baking soda
  • 4.8 g stevia powder

Wet Ingredients

  • 74 g allulose , granulated
  • 93 g egg , room temp
  • 186 g fat-free Greek yogurt , room temp
  • 108 g applesauce , unsweetened, room temp
  • 45 g butter , melted
  • 9.6 g vanilla extract

Brown Sugar Topping

  • 25 g allulose granulated
  • 10 g all-purpose flour
  • 4 g molasses
  • 6 g softened butter


  • Preheat oven to 425F / 220C
  • Add all wet ingredients (including granulated allulose) and whisk well (use an electric mixer if you have one).
  • Sift together all dry ingredients (except blueberries) in a separate bowl, then add to wet ingredients and mix until combined. Cover and refrigerate for at least 30 minutes.
  • Prepare muffin pan with liners, then add ~20g of plain batter into each muffin.
  • Toss blueberries in a small amount of flour to coat, sift off excess, then add to remaining batter, fold them in, and scoop evenly into each muffin.
  • Prepare brown sugar topping by mixing all ingredients together with a fork (or pastry cutter), then sprinkle evenly over all muffins
  • Place in oven for 7 minutes at 425F / 220C, then reduce heat to 350F / 175C and bake for another 12 minutes.
  • Let cool in pan for 5 minutes, then remove and place on wire rack. Enjoy hot or let them cool completely.



  • You can use granulated erythritol, but I much prefer allulose.
  • Recommend using an over thermometer to make sure your oven actually reaches the desired temperatures (including cracking the door and letting a little heat out to bring temperature down to 350F / 175C)
  • Egg measurement is important and doesn’t always come out to whole numbers of eggs. The eggs I have from Costco are ~50g each. So you could use two for this recipe. But I recommend cracking two into a bowl, whisking them, and measuring out the proper amount.
Keyword Blueberry, Muffins

Why This Protein Muffin Recipe Works

protein blueberry muffins rising in the oven

All-purpose flour and protein powder blend

This muffin recipe uses all-purpose flour to maintain a traditional muffin taste and texture while adding in a blend of whey protein powder and collagen protein to improve the macros.

Easy to prepare

The recipe is easy enough, even if it’s your first time baking. With some mixing, refrigerating, and heating, you can enjoy hot and delicious protein blueberry muffins in no time!

Low Sugar Content

Instead of refined sugar, this recipe uses granulated allulose, stevia powder, and corn fiber for sweetness.

Ingredients & Substitution Options

The ingredients in this healthy blueberry muffin recipe have been carefully selected to balance the taste, texture, and macros. If you’re regularly baking healthy recipes, you’ll want to have all of these stocked in your pantry.

All-purpose flour

As mentioned above, I’ve included just enough all-purpose flour to keep that classic muffin taste and texture. You can add a bit of whole wheat flour for additional fiber, but I haven’t tried this as I’m completely fine with white flour.

Whey protein powder

When it comes to baking with protein powder, all of them contribute differently to the result. Whey protein can make a baked good dry, but with the proper hydration and quantity, it adds lightness and fluffiness. When unflavored, it adds flavor as milk would. If you only have vanilla protein powder on hand, that will work too, but the taste isn’t as “clean,” in my opinion. It is possible to substitute with a plant-based protein powder, but you’ll have to adjust your liquid ingredients and baking time.

Greek yogurt

Greek yogurt is one of the most versatile ingredients for protein baking. It adds a bit of acid (as buttermilk would), a ton of added protein, extra moisture, and very few other calories.

Stevia powder

Pure stevia powder keeps the muffins’ sweetness, but unlike sugar, it doesn’t have calories or carbohydrates. You also only need a bit of it because it’s 200-350x sweeter than table sugar. Note that you’ll need a bulking agent (such as granulated allulose) if you plan to completely replace sugar in your baked goods.

Granulated allulose

Using granulated allulose (instead of only stevia) increases the muffins’ ability to hold moisture, so they bake evenly, with less early browning. This makes the muffin chewy and soft, with a good texture and even sweetness. Aside from using allulose, you could use granulated erythritol.

Unsweetened apple sauce

Did you know that applesauce is an excellent substitute for oil and butter? This allows us to reduce fat and calories without losing moisture. It also has natural sugar that adds sweetness to the muffins. Canned pumpkin can also be an alternative to oil and butter, but if you do, you’ll probably need to add some extra sweetener.

Collagen protein

A great way to boost the protein content of baked goods without the risk of them drying out is by using collagen protein. Like granulated sugar, collagen is hygroscopic and gels when mixed with liquid. It doesn’t provide structure but is an ideal and healthy thickener.

Corn fiber

I suggest you add fiber to these low calories Blueberry Protein Muffins recipe to add volume without much calories and to make you feel full longer. Corn fiber is only 8 calories per 10 grams versus 40 calories per 10 grams for carbs or protein. Aside from helping thicken food, it’s also a great fiber choice for sweet baked goods as it has no grittiness and adds a little bit of sweetness.

Xanthan gum

Because we’re swapping out all-purpose flour with whey protein and collagen protein, we are losing structure from the starch and gluten. We’re not adding gluten back in because that’s not what we want for muffins, but we do need more structure. That’s when xanthan gum comes into the picture. Without it, the blueberries will sink to the bottom of the muffins and the muffins will collapse when they come out of the oven.

Customizations for Different Types of Protein Muffins

Buckle up! This Blueberry Protein Muffins recipe is not limited to just blueberries. It’s infinitely customizable, and you can tweak the muffin base with a bit of effort to create any type of muffin you’re craving. 

Here are other high-protein recipes you can try:

Banana Protein Muffins

Remember those bananas you bought, left in your kitchen, and just discovered now? You know, those brown and spotty ones? Yep. They are perfect for making banana protein muffins! Throw some mashed bananas in the recipe above, and you’re all set. It’s an excellent breakfast to munch on during busy mornings, too!

Apple Protein Muffins

Now there’s something to look forward to after your workouts — apple protein muffins. Simply replace the blueberries with apples, or go all out adding cinnamon, molasses, and applesauce with our Protein Apple Cinnamon Muffins recipe.

Healthy Chocolate Chip Protein Muffins

Who says you can’t make healthy baked goods with chocolate? We all need to hit that daily nutrition serving intake, but that doesn’t mean you should restrain yourself. Especially not if it’s for chocolate and more so if you can make it healthy! Mix sugar-free chocolates, protein powder, and unsweetened applesauce with the other ingredients above, and enjoy!

Different Toppings to Try

  • Oat crumble topping – Think of Streusel Crumb topping, but make it healthier.
  • Fruit toppings – You can use blueberries, a mix of berries, lychee, and other fruits.
  • Nothing – These blueberry protein muffins taste delectable on their own.

Make them lower calorie

  • Use egg whites instead of whole eggs.
  • Replace the butter with more apple sauce.

Make them higher protein

  • Replace the all-purpose flour with more whey and collagen powder.

Expert Tips for Blueberry Protein Muffins with Brown Sugar Crumble

Use a Cookie Scoop

Because this batter is sticky from the xanthan gum, we’ve found it very helpful to use a cookie scoop to get the batter from the bowl to the muffin tin.

Do Not Under or Overmix

Make sure to mix your dry and wet ingredients. Try not to overmix your muffin butter, but carefully check that there’s no dry flour left unmixed. 

Coat Blueberries with Flour

Make sure to coat the blueberries with a little bit of flour. This helps prevent their juices/color from bleeding into the rest of the batter. It also helps prevent them from sinking, but the verdict is still out on that one. Look out — I’ve got a different technique for that.

Pour Some Batter into the Muffin Tin

Before you gently fold in the blueberries, put a small amount of batter into each spot in the muffin tin. This creates a foundation, a blueberry-less portion that helps prevent them from sinking to the bottom. After you’ve filled all spots in the muffin tin, you can fold in the blueberries and proceed.

Check with Toothpick

To check if your muffins are done, try inserting a toothpick into the center of your blueberry muffin. If the toothpick comes out clean or only a few crumbs are left, then your muffins are ready.

Bulk Prepping & Storage Tips

Store in a Sealed Container

Your homemade blueberry muffins can be stored in a sealed container for about 2 days at room temperature. Put some paper towels on the bottom and top of the muffins to preserve their freshly-baked taste.

Cool the Muffins for Freezer Storage

If you want to store your leftovers in a freezer, cool them completely first. Put them in an airtight and freezer-safe bag. Your muffins can last up to 2 to 3 months if stored properly in the freezer. You should flash-freeze them before putting them together in the bag for the best results.

Reheat and Serve

These muffins can be reheated in a few seconds in the microwave, or you can even try reheating them in an air fryer or toaster oven.

Frequently Asked Questions

Can you use frozen blueberries instead of fresh blueberries?

You can use frozen blueberries in place of fresh ones. However, when using frozen blueberries, you may need to add a few minutes to the baking time to ensure the muffins cook through. 

Frozen blueberries also tend to bleed more than fresh blueberries, which may result in a slightly different color in the finished muffins. To minimize bleeding, rinse the frozen blueberries under cold water and pat them dry before adding them to the muffin batter.

Overall, frozen blueberries are a convenient alternative to fresh blueberries, especially when fresh blueberries are out of season or not readily available.

Is protein powder damaged when it is baked?

No. Our bodies absorb the same amount of protein, which isn’t damaged when baked or cooked. Although it can be denatured once it enters the body, and we may find it harder to digest at times, the macro will not be affected.

Are muffins a healthy breakfast choice?

Yes, if you make it yourself with healthy ingredients, muffins are excellent breakfast options. There are more high-protein recipes out there that you can try to create your own muffin, like the Blueberry Protein Muffins recipe I just shared with you. Note that, in general, muffins are high in fat and sugar, so it will depend on the breakfast cuisine and ingredients you prefer.

Can these Blueberry Protein Muffins be made with lower calories?

Yes. There are two easy ways to lower the calories of the recipes which we presented above. One, you can use egg whites instead of whole eggs, and two, you can replace butter with additional apple sauce.

Can these be made into even higher protein muffins?

Yes. You can replace some of the all-purpose flour with additional whey and collagen powder. However, keep in mind replacing too much could ruin the final result.

Why are protein muffins dry?

Other protein recipes may lead you to a dry batch of muffins because of too much oat flour, almond flour, or protein powder. So be sure not to overpour the dry ingredients. Another factor that can make protein muffins dry is the oven temperature. See that you don’t bake your muffins at low temperatures for too long.

Don’t worry, my recipe will not lead you astray. I made sure to add the right amount of flour, butter, granulated allulose, and applesauce to make the muffins come out moist and fluffy.

How much protein is in a blueberry muffin?

Regular blueberry muffins have 6 grams of proteins. Compare this with the 0.8 grams per body kilogram, and we’ll realize the lack of protein in regular blueberry muffins. To easily get the daily protein intake needed, these Blueberry Protein Muffins contain 13 grams each.


These Protein Blueberry Muffins with Brown Sugar Topping are a perfect breakfast or snack option that you don’t want to miss out on. With their high protein content and taste, they’re sure to become a new favorite in your kitchen!

The recipe is simple and straightforward, with easy-to-find ingredients, making it an ideal choice for those looking to try their hand at baking. Plus, adding the brown sugar topping takes these muffins to the next level of deliciousness!

Whether you’re looking for a healthy breakfast, a tasty afternoon snack, or a treat to share with family and friends, these Protein Blueberry Muffins with Brown Sugar Topping are perfect. So, what are you waiting for? Get your ingredients together and start baking – you won’t regret it!

Stay tuned for more healthy breakfast recipes!

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