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High Protein Blueberry Cheesecake Muffins

Have you ever had a muffin with a layer of cheesecake in the center? If not, get ready to have your world rocked by these blueberry cheesecake muffins. 

Each muffin has a high protein blueberry cheesecake filling wrapped inside a low fat blueberry muffin. Sounds crazy, right?

What’s even crazier, though, is that each muffin has just 135 calories! 

two images of blueberry cheesecake muffins with one cut in half to show the cream cheese filling and title text on a center banner

I always like to give inspiration credit and in this case, my blueberry cheesecake muffins were inspired by these blueberry cream cheese muffins by Dorothy at Crazy for Crust. 

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Ingredient Substitutions and FAQ about These Blueberry Cheesecake Muffins

I originally posted this recipe on my Instagram and will quickly answer the most common recipe modification questions I received in the section below. 

What can I substitute for all purpose flour? 

Whether you need a gluten free or simply lower carb alternative, my typical recommendation is swapping almond flour gram for gram. That said, every recipe is a bit different. 

In my low carb skillet cookie recipe, for example, a 1:1 swap worked perfectly. But with my low carb lemon protein cookies, I needed an extra tablespoon of Greek yogurt and slightly less baking powder. 

low carb skillet cookie with protein powder

I’d recommend starting with 1:1 and increasing or reducing liquid ingredients as needed to get your muffin batter just right. 

Can I use a different flavor of protein powder?

The recipe calls for a new flavor of Bowmar Nutrition protein powder, Blueberry Cheesecake. But you’re more than welcome to use another flavor. There are still blueberries in the muffins, after all. 

I used Bowmar Nutrition’s Frosted Cookie protein powder in my white chocolate raspberry protein cheesecake and would recommend that for a vanilla style cheesecake filling. 

4 photos of the process of making blueberry cheesecake muffins

Is there a substitute for unsweetened apple sauce? 

I use apple sauce in place of fat sources in my lower calorie baked goods. If you don’t have access to apple sauce or wanted to use something else, light butter or a whole egg would be easy substitutes.  

For a plant based substitute, a bit of oil, canned pumpkin, or another fruit puree should do the trick since it’s only 1/4 cup. 

P.S. If you’re worried about tasting the apple sauce, I can assure you 1/4 cup won’t be noticeable! 

a blueberry cheesecake muffin cut in half to show a layer of cheesecake inside

What’s the deal with the net carbs in Swerve Granular? 

In the original Instagram post, I mentioned that using Swerve in the muffin batter added 5 grams of carbs per muffin because I have some readers that follow net carbs and some that track every carb. 

Swerve is made from erythritol, which is one of those tricky sugar substitutes that classifies as a zero-calorie, non-glycemic carb. So the calories from its carb content are so low it rounds down to zero. 

Should I track net carbs or calories?

It’s tricky, but my recommendation is if you track calories, treat something like Swerve products as zero-calorie. And if you track macros, log the carbs and be happy with a tiny hidden calorie deficit bonus. 

Essentially, track what’s on the label and move on. Don’t drive yourself crazy over something so small. 

a pyramid of high protein blueberry cheesecake muffins

Also, it’s worth noting you can use any granulated sugar substitute like a baking stevia. Whatever you use, make sure it subs 1:1 for sugar like Swerve does. 

Are there a substitutes for the Greek yogurt and cream cheese to make these blueberry cheesecake muffins dairy free? 

I use Greek yogurt in lower calorie recipes as another fat replacement. If you wanted to use a plant based oil, I’d recommend using 1 cup in place of the Greek yogurt. Similar to my almond flour suggestion above, it may take some tinkering to get things just right. 

For the cream cheese, I’d recommend a plant based cream cheese product. 

And if you’re wondering where to find fat free cream cheese, I buy mine from Walmart and/or Kroger. If you can’t find any, feel free to use 1/3 fat cream cheese. There’s only 4 ounces in the recipe so the fat differences won’t make a huge calorie difference. 

3 photos of reader made blueberry cheesecake muffins

3 reader re-creations from @erika_broooke, @grantreiman, and @txdevon on Instagram!

How do you store these blueberry cheesecake muffins?

After the muffins have baked, you’ll want to cool and refrigerate to let the cream cheese set. I’d recommend leaving the muffins refrigerated for up to 3-5 days.

You can reheat the muffins in the oven (a few minutes at 350), an air fryer (same as oven), or microwave (15-20 seconds) before eating. Or you can eat them cold! 

Final Recipe Notes for Blueberry Cheesecake Muffins

I mentioned that I posted this recipe on Instagram first so if you’d like to get in on the action there you can find me @mason_woodruff. Or you can join my free Facebook group and get ideas and tips from other Proton Party members.

a pyramid of high protein blueberry cheesecake muffins

Blueberry Cheesecake Muffins

Yield: 9 muffins
Prep Time: 15 minutes
Cook Time: 25 minutes
Total Time: 40 minutes

Low fat blueberry muffins filled with protein cheesecake. 


Blueberry Muffins

  • 1 C (120g) All Purpose Flour
  • 1/4 C Granular Sweetener, I used Swerve Granular
  • 1 tsp Baking Powder
  • 2 large Eggs
  • 3/4 C (168g) Vanilla Fat Free Greek Yogurt
  • 1/4 C (60g) Unsweetened Apple Sauce
  • 3/4 C (120g) Fresh Blueberries, if frozen, microwave 45-60 seconds first and expect slightly blue muffins

Cheesecake Filling

  • 4 oz Fat Free Cream Cheese, or 1/3 fat
  • 1/4 C (56g) Vanilla Fat Free Greek Yogurt
  • 2 scoops (56g) Protein Powder, I used Bowmar Nutrition Blueberry Cheesecake


  1. Preheat an oven to 350F and place 9 silicone muffin cups on a baking sheet or spray 9 slots in a 12-muffin tin with nonstick cooking spray.
  2. Mix the muffin ingredients together in a large bowl before folding in the blueberries. Set aside. blueberry muffin batter mixed together
  3. Microwave the cream cheese for 60 seconds before stirring in the Greek yogurt and protein powder. Mix until smooth. cream cheese and Greek yogurt in a mixing bowl with protein powder on top
  4. Add 2 tablespoons of the muffin mixture to each of the baking cups, filling them about 1/3 full. IMPORTANT: Do your best to limit the amount of blueberries on the bottom layer to avoid a soggy bottom and have more blueberries on top after the muffins bake. 
  5. Spoon about a tablespoon of the cream cheese mixture on top of the muffin layer. the protein cheesecake filling on top of the first layer of blueberry muffin batter
  6. Spoon the remaining muffin mixture on top of the cream cheese layer. the top layer of blueberry muffin batter in silicone baking cups
  7. Bake for 20-22 minutes or until the tops are golden brown.
  8. Remove to cool. The muffins are best when fully cooled and refrigerated for 30-60 minutes to allow the cream cheese filling to set.


  • Each muffin has 2 Smart Points.
  • Each muffin has 17g net carbs or 22g of carbs with Swerve. If you use something like baking stevia, each muffin should have 17g of carbs. 
  • If you have ingredient substitution questions about all purpose flour, cream cheese and Greek yogurt, or the Swerve/sweetener, check the FAQ for each ingredient in the post above. 
Nutrition Information:
Yield: 9 muffins Serving Size: 1 muffin
Amount Per Serving: Calories: 135Total Fat: 1.5gCarbohydrates: 17gProtein: 12g

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More Protein Muffins You Might Like

Looking for a lower carb muffin recipe? Check out my 6-ingredient pumpkin protein muffins. Each one has just 4 grams of carbs.

low carb pumpkin protein muffins

And if you’re a banana bread fan, my pumpkin banana bread protein muffins are to die for! 

healthy pumpkin banana bread muffins


Monday 7th of June 2021

All this needs is some lemon zest or lemon extract! Fantastic recipe!

Kelli T

Tuesday 21st of July 2020

Thank you so much for making a macro friendly version of one of my favorite muffins! I've been making these a few times a month and feel like I'm cheating every time I get to eat them. I subbed a high protein pancake mix for the flour and use blueberry nonfat yogurt and vanilla PEScience protein powder. They still come out amazing! Topped with a bit of lemon nut butter and every bit tastes like heaven!


Wednesday 15th of April 2020

These are amazing!! I used PEScience cake pop protein for the filling since that’s what I had available and they turned out great! I think it was a perfect pair with the fresh bluebs already in the muffin. Also went with Almond flour instead of all purpose flour so I appreciate that you add substitution options on all of your blogs!👌


Sunday 24th of November 2019

These have been my favorite muffins. I love cheesecake and honestly the center is a perfect consistency. I have made these for multiple events and they are always a hit!

Anna Laumann

Wednesday 10th of April 2019

Guys... these are even more amazing than they look. He has done it again!

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