High-Protein Gluten-Free Muffins for Meal Prep

These gluten-free, high-protein muffins make an excellent snack without any cottage cheese. They’re made with almond flour, dairy-free Greek-style yogurt, and an optional blackberry frosting for a touch of sweetness.

High protein muffin being held in a hand with a bite taken out of it.

Why you’ll love these high-protein muffins

A reader once asked for a protein-and-fiber muffin that included psyllium husk, and this recipe is the result. It’s a hearty, protein-packed snack that’s also gluten-free and dairy-free (if you choose a dairy-free yogurt and protein powder).

Protein desserts and snacks are popular right now, and these muffins deliver protein without relying on cottage cheese. They’re handy for busy mornings, lunches, or as a satisfying snack for kids and adults alike.

Here’s what makes these muffins special:

Headshot of Michelle Hoover, a brunette woman with pigtails in a pink sweater.
  • No cottage cheese. The protein comes from dairy-free protein powder and a thick, Greek-style dairy-free yogurt.
  • Psyllium husk adds fiber and structure. Psyllium acts as a binder and boosts fiber content, helping the muffins hold together and feel satisfying.

Quick Overview

  • Servings: 6 muffins
  • Calories: 273 per muffin
  • Protein per serving: 16.3 g
  • Difficulty: Easy
  • Diet types: Gluten-free, dairy-free (with appropriate ingredients), refined sugar–free
  • Flavor notes: Comforting, lightly sweet, with a mild berry tang if you use the optional frosting

Table of contents

  • Why you’ll love these high-protein muffins
  • Quick Overview
  • Recipe Ingredients
  • How to Make High-Protein Muffins
  • Michelle’s Tips & Tricks
  • Other Gluten-Free Muffin Recipes to Try…

Recipe Ingredients

See the recipe card below for exact amounts and full instructions.

The ingredients to make high protein muffins on a counter before baking begins.
  • Dairy-free protein powder: Choose a neutral-flavored or vanilla dairy-free powder to boost protein.
  • Almond flour: Provides structure and a tender crumb; this recipe has not been tested nut-free.
  • Psyllium husk: Adds fiber and helps bind the batter.
  • Eggs: If you need an egg-free option, try two flax eggs, though texture may vary.
  • Applesauce & coconut sugar: Applesauce replaces oil for moisture, while coconut sugar adds gentle sweetness.

How to Make High-Protein Muffins

Below are the main steps so you can see the process at a glance. Full details and measurements are in the recipe card.

A white ceramic bowl filled with batter to make high protein muffins.

Step One. Whisk the applesauce, eggs, dairy-free yogurt, and coconut sugar until smooth. In a separate bowl, combine almond flour, psyllium husk, protein powder, baking powder, and cinnamon. Pour the wet mixture into the dry and stir until a batter forms.

A muffin tin with a freshly baking high protein muffin in it.

Step Two. Spoon the batter into prepared muffin liners (fill about three-quarters full). Bake until set and lightly golden, then remove and cool.

A glass bowl with a yogurt blackberry icing mixture being mixed by a spoon.

Step Three (icing). Simmer blackberries with a little water, mash, and strain to extract juice. Mix the juice with dairy-free Greek-style yogurt and sifted powdered sugar to make a thin frosting.

A hand dipping a high protein muffin into the greek yogurt icing in a glass bowl.

Step Four. Dip the muffin tops into the yogurt mixture for a thin coating, let set, then enjoy. The icing is optional—the muffins are great plain, too.

Michelle’s Tips & Tricks

  • Let the muffins cool completely. Protein powder can make the crumb slightly sticky when warm, so cooling helps them release from liners cleanly.
  • Spray liners well or use a silicone pan. This prevents sticking and preserves the muffin shape when you remove them.

Other Gluten-Free Muffin Recipes to Try…

  • Lemon Zucchini Poppyseed Muffins
  • Chocolate Banana Bread Muffins (gluten-free)
  • Carrot Cake Muffins

If you tried these High Protein Muffins or any other recipe, please leave a star rating and let me know how it went in the comments. Thanks for visiting!

Gluten Free High-Protein Muffins
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Gluten Free High-Protein Muffins

Yield: 6 muffins
Prep Time: 10 mins
Cook Time: 20 mins
Author: Michelle
These gluten-free high-protein muffins provide a convenient protein boost without cottage cheese. They pair well with coffee, yogurt, or a piece of fruit.

Ingredients

For the muffins

  • 2 eggs
  • ½ cup applesauce
  • ¼ cup dairy-free Greek-style 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
  • cup dairy-free Greek-style yogurt
  • 2 tsp powdered sugar

Instructions

For the muffins

  • Preheat oven to 350°F and line a 6‑cup muffin tin. Spray liners or use a well-greased silicone pan.
  • Whisk applesauce, eggs, dairy-free yogurt, and coconut sugar until combined.
  • In another bowl, mix almond flour, psyllium husk, protein powder, baking powder, and cinnamon. Combine wet and dry ingredients until a batter forms.
  • Divide batter among liners, filling about 3/4 full.
  • Bake 20 minutes or until muffins are set and firm. Remove and cool on a rack for at least 30 minutes before adding optional icing.

For the icing (optional)

  • Combine blackberries and water in a small pot. Simmer gently for about 5 minutes, mash, then strain to collect juice.
  • Whisk yogurt with powdered sugar, then add 2 teaspoons of the blackberry juice and whisk until smooth. (Reserve any extra juice for drinks.)
  • Dip muffin tops into the yogurt mixture for a thin frosting. Let set and top with fresh berries if desired.

Notes

The icing is optional; the muffins are delicious plain. Nutritional facts listed do not include the icing.
Serving: 1muffin,
Calories: 273kcal,
Carbohydrates: 27.9g,
Protein: 16.3g,
Fat: 13.1g,
Fiber: 7.1g
All nutrition facts are estimated and will vary.

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