Gluten Free High-Protein Muffins
These gluten-free high-protein muffins are the perfect protein snack without cottage cheese! They’re made with almond flour, dairy-free yogurt, and a blackberry frosting.

Why you’ll love these high-protein muffins
A few years ago, a reader sent me an amazing request for a protein-and-fiber muffin with psyllium husk. I don’t remember exactly what I said at the time, but the request stuck with me as incredible, and I finally got around to it!
Protein desserts and snacks are all the rage, and though I do generally prefer to just eat dessert, I do love sneaky protein like my protein ninja creami ice cream. And having a protein muffin has really come in handy with a picky kid at home!
These gluten-free high-protein muffins are an amazing snack that you need to try! Here’s why you’ll love it…

- No cottage cheese. It seems like every high-protein recipe has cottage cheese these days, but these don’t! The protein comes from dairy-free protein powder and Greek-style coconut yogurt.
- Psyllium husk for extra fiber. Psyllium husk is often used as a binder in recipes, but it also adds an amazing boost of fiber.
Quick Overview
- Servings: 6 muffins
- Calories: 273
- Protein per serving: 16.3g
- Difficulty: Easy
- Diet types: Gluten-free, dairy-free & refined sugar free
- Flavor notes: Comforting and slightly sweet
Table of contents
Recipe Ingredients
See the recipe card below for full information on ingredients and quantities.

- Dairy-Free Protein Powder. I prefer to use this dairy-free protein powder for this recipe!
- Almond Flour. I haven’t successfully made this recipe nut-free.
- Psyllium Husk.
- Eggs. I haven’t tried to make this recipe with an egg substitute, but I would recommend 2 flax eggs.
- Apple Sauce & Coconut Sugar. This adds a sweetener to the muffins, and the applesauce also works as a swap for oil.
How to Make High-Protein Muffins
Here are the simple steps, with photos, to make this recipe. Find full instructions in the recipe card.

Step One. Combine the applesauce, eggs, yogurt and coconut sugar. Then combine the almond flour, psyllium husk, protein powder, baking powder, and cinnamon in another bowl. Pour the wet ingredients into the dry ingredients and stir until a batter forms.

Step Two. Spoon the batter into the muffin liners and bake. Remove from oven and let cool before icing.

Step Three. Combine blackberries and water to a small pot, simmer and strain. Then add the yogurt, powdered sugar, and blackberry juice to a bowl and whisk.

Step Four. Dip the tops of the muffins into the yogurt to form a thin frosting. Enjoy!
Michelle’s Tips & Tricks
- Let the muffins cool! Baked goods with protein powder tend to get sticky and can stick to muffin liners, but letting them sit for a while helps them come out of the liners more easily.
- Make sure you spray the muffin liners. Again, they can stick to the muffin liners, so be sure to spray them well with oil!
Other Gluten-Free Muffin Recipes to Try…
If you tried these High Protein Muffins or any other recipe on my blog please leave a star rating and let me know how it went in the comments below. Thanks for visiting!

Gluten Free High-Protein Muffins
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Ingredients
For the muffins
- 2 eggs
- ½ cup applesauce
- ¼ cup dairy free Greek yogurt
- ¼ cup coconut sugar
- 1 cup almond flour
- 2 tbsp psyllium husk
- 2 scoops dairy free protein powder
- 2 tsp baking powder
- 1 tsp cinnamon
Blackberry yogurt icing
- ½ cup blackberries
- 2 tbsp water
- ⅓ cup dairy free Greek yogurt
- 2 tsp powdered sugar
Instructions
For the muffins
- Preheat the oven to 350 F and add 6-7 muffin liners to a muffin tin. Spray well with spray oil.
- Combine the applesauce, eggs, yogurt and coconut sugar in a bowl and whisk well.
- Combine the almond flour, pshyllium husk, protein powder, baking powder, and cinnamon in another bowl. Pour the wet ingredients into the dry ingrededients and stir until a batter forms.
- Spoon the batter evenly into the muffin liners, filling about 3/4ths of the way.
- Transfer to the oven and bake for 20 minutes or until the muffins are set and firm.
- Remove from the oven and allow to cool on a cooling rack for at least 30 minutes (preferably longer) before adding optional icing.
For the icing (optional)
- Add the blackberries and water to a small pot. Bring to a low simmer and carefully mash the blackberries. Simmer for 5 minutes and strain.
- Add the yogurt to a bowl and sift the powdered sugar over the yogurt. Whisk to combine. Add 2 tsp of the blackberry juice and whisk again.
- Dip the tops of the muffins into the yogurt to form a thin frosting. Set aside and allow to set, topping with fresh blackberries if desired!