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Gluten Free Coffee Cake Protein Muffins

This recipe combines protein powder with almond and oat flour to make cinnamon coffee cake muffins that you’ll never know are gluten free. They’re topped with a walnut oat streusel and sugar free glaze. And each muffin has 8 grams of protein with just 120 calories each! 

coffee cake muffins on a wire rack

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Coffee Cake Muffins Recipe Walkthrough

While the ingredient list may look lengthy, this is really a fairly straightforward recipe. I’ll run you through from start to finish below and touch on ingredient substitutions as we go. If you have an ingredient question I don’t cover, feel free to drop a comment below. 

And if you’re in a hurry, you can find the printable recipe card at the bottom of the post. 

Step 1: Making the protein muffin batter.

dry ingredients for protein muffins mixed together and an egg, milk, and apple sauce mixed together

Mixing the dry and wet ingredients separately ensures even distribution of the dry ingredients and prevents over mixing once you add wet to dry. Read: it makes for easier work and superior muffins. 

Can I use a different protein powder?

This is always the first question that pops up in my protein powder recipes, and my answer is always the same.

No protein powder is the same so substitute at your own risk.

I know, it’s not fair. The recipe calls for vanilla PEScience Select which is a blend of whey and casein. If you’re using a whey-only protein you’ll probably need to use more protein powder to achieve the same batter consistency you see in the photos below. 

Side note: If you’re looking to get into protein powder baking, you can use my affiliate discount code mason to save 15% on PEScience products. You can even order single serving or 5-serving samples to try these coffee cake muffins or others like my snickerdoodle muffins or Oreo protein cake.

I don’t have any oat flour on hand. Can I make my own? 

You bet. Just throw some oats in a food processor and blend until they resemble flour. The recipe calls for 60 grams or 1/2 cup of oat flour. If you don’t have a food scale, that’s about 3/4 cup of whole grain oats. Get a food scale, by the way. I have my favorites in my kitchen tools Amazon list

mixed protein muffin batter and 9 silicone muffin molds on a baking sheet

What is Swerve?

Swerve sweeteners are a line of zero-calorie, erythritol-based sugar substitutes that taste, measure, and cook just like sugar. This recipe actually calls for three of their products. If you don’t have them on hand, you can use the real deal with minor nutrition facts changes or other sugar substitutes as long as they measure 1:1 for sugar. 

You can learn more about Swerve on their FAQ page

Do I have to use almond milk? 

Nope. You should be able to use any milk for your muffins. 

Is there a substitute for apple sauce?

I’ll start by saying you’ll never know it’s there. But if you need a substitute, canned pumpkin is a great option. Both of these work as what I like to call fat replacements. So instead of using butter or oil for moist bake goods, these are a much lower calorie option. 

If you don’t have either on hand, use another egg or some fat via light butter or even something like whole milk. 

Step 2: Making the walnut streusel. 

coffee cake muffin batter in silicone molds beside a bowl of walnuts, oats, butter, and brown sugar

The streusel here is basically the same as the one from my pumpkin banana bread muffins with a few extra walnuts. You’ll see another Swerve product here in their brown sugar substitute.

Again, you could use real brown sugar or maybe even a little honey, vanilla extract, or sugar free pancake syrup. Just try not to oversaturate the top of the muffins. 

coffee cake protein muffins with streusel added before baking

A quick note on filling the baking cups: If you’re using a muffin tin or mold, the size may affect the number of muffins this recipe yields. Instead of overfilling, simply make an extra muffin and vice versa. 

Step 3: Baking, cooling, and making the sugar free glaze. 

coffee cake protein muffins after baking

Whew, that’s it. One thing I always like to mention with protein powder recipes is the importance of not over baking them. A higher protein content means that your muffins can go from light and fluffy to tough and chewy if you’re not careful.

So check on your muffins early and take note of smaller/larger muffin molds. 

The glaze is a simple 2-ingredient combo with yet another product from the Swerve lineup—their confectioners powdered sugar substitute. I think you get it by now, but you could use real powdered sugar if you lack the Swerve. You could also try making your own powdered sugar substitute with Swerve granular + a thickener like corn starch, arrowroot powder, tapioca flour, or maybe even some extra protein powder. 

You could also skip the glaze altogether! 

Welp, that should cover everything. If you need to know anything else about these coffee cake protein muffins, drop a comment below the recipe card or hop in my free Facebook group to get some assistance from the 13,000 healthy home cooks there!

Gluten Free Coffee Cake Protein Muffins

Gluten Free Coffee Cake Protein Muffins

Yield: 9 Muffins
Prep Time: 15 minutes
Cook Time: 30 minutes
Total Time: 45 minutes

120-calorie cinnamon coffee cake muffins topped with a walnut oat streusel and sugar free glaze.


For the Muffins

  • 2 scoops (62g) PEScience Select Protein Powder, vanilla
  • 1/2 C (60g) Oat Flour*
  • 1/4 C (30g) Almond Flour
  • 2 Tbsp (24g) Swerve Granular (or granulated sugar)
  • 2 tsp Baking Powder
  • 2 tsp Ground Cinnamon
  • 1/4 tsp Kosher Salt (or 1/8 tsp table salt)
  • 1 large Egg
  • 1/2 C (120mL) Almond Milk (or your choice of milk)
  • 1/4 C (60g) Unsweetened Apple Sauce

For the Streusel

  • 1/4 C (30g) Chopped Walnuts
  • 2 Tbsp (10g) Rolled Oats
  • 2 Tbsp (24g) Swerve Brown (or brown sugar)
  • 2 Tbsp (28g) Light Butter

For the Glaze

  • 1/4 C (36g) Swerve Confectioners (or powdered sugar)
  • 3-4 tsp Water


  1. Preheat an oven to 350F and place 9 silicone baking cups on a baking sheet or spray a muffin tin with nonstick cooking spray. Set aside.
  2. Mix the dry ingredients for the muffins together in a large bowl. In a separate bowl, whisk together the egg, milk, and apple sauce together before adding to the dry ingredients. Stir the muffin batter until smooth.
  3. Fill each baking cup 3/4 full with the muffin batter. Set aside.
  4. Add the butter, walnuts, oats, and Swerve brown to another bowl and stir together before adding to the top of each baking cup.
  5. Bake for 25-30 minutes until a toothpick or knife comes out clean. Transfer the muffins to a wire rack to cool.
  6. For the glaze, mix the Swerve confectioners and water together and drizzle over the top of the cooled muffins.


*If you're concerned with cross contamination, be sure to buy dedicated gluten free oat flour or whole grain oats to make your own oat flour.

Nutrition Information Notes

  • Each muffin has 3 WW Smart Points (blue plan).
  • Nutrition facts do not include carbs from the zero-calorie Swerve sweeteners. Erythritol has 0.2 calories per gram which would add 16.8 calories to the entire recipe or 1.9 calories to each muffin.
Nutrition Information:
Yield: 9 Muffins Serving Size: 1 Muffin
Amount Per Serving: Calories: 120Total Fat: 7gCarbohydrates: 8gProtein: 8g

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Monday 8th of May 2023

Nevermind on my comment on casein, I should have read the blog more carefully ;)


Monday 8th of May 2023

I only have casein protein powder - how would I adjust the recipe?


Sunday 20th of February 2022

These are absolutely delicious! 9 muffins are NOT enough! I made a quad match the very next day! I skipped the walnuts.

Anne S

Sunday 23rd of January 2022

My family loved them! They are demanding more! 😃


Wednesday 24th of November 2021

Not sure what part of these taste like "coffee" but let me try them

Mason Woodruff

Wednesday 24th of November 2021

In the US, coffee cake is typically just a sweet cake with a streusel on top intended to be served with your morning coffee. It's a little different than a coffee-infused cake. Hope that clears up the confusion!

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