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These apple cinnamon protein muffins are everything you love about cozy fall baking. With sweet apples, warm spices, and a soft, high-protein crumb that keeps you full for hours. Made with Greek yogurt, cinnamon applesauce, and vanilla protein powder, they're the perfect grab-and-go breakfast or post-workout snack!
Why You'll Love These Apple Cinnamon Muffins
If you've been looking for a healthy breakfast muffin that tastes like dessert but powers your morning, this one's for you! These muffins combine real apple flavor, wholesome gluten-free flour, and protein powder for a nourishing start to your day.
The batter comes together in one bowl (no mixer needed!) and bakes into golden-brown perfection in under 25 minutes. Whether you're meal prepping for busy mornings or stocking your freezer for quick snacks, these muffins make high-protein baking simple and delicious!
If you're new to gluten-free baking, these muffins are a foolproof place to start! Simple, cozy, and so satisfying. For more healthy breakfast ideas, check out my Easy Vegan Baked Oats with Protein Powder or Healthy Banana Protein Muffins.
Ingredients You'll Need
- Coconut oil: Adds moisture and richness.
- Cinnamon applesauce: Sweetens naturally and keeps the muffins soft.
- Plain fat-free Greek yogurt: Boosts protein while keeping them fluffy.
- Maple syrup: A touch of natural sweetness.
- Eggs: Bind the ingredients for a tender texture.
- Vanilla extract: Enhances flavor.
- Gluten-free 1:1 flour: I like the King Arthur Baking brand for consistent results. These muffins work well with almond or oat flour blends for extra fiber.
- Coconut sugar: Adds caramel-like sweetness without refined sugar.
- Vanilla protein powder: Choose your favorite brand. I used Clean Simple Eats – use code MARY10 for a discount! This recipe works with whey or plant protein.
- Cinnamon: Brings that classic fall warmth.
- Baking powder and baking soda: Help the muffins rise.
- Salt: Balances the sweetness.
- Finely diced apple: Adds juicy bites in every muffin.
How to Make These Apple Cinnamon Protein Muffins
Step 1: Preheat the oven to 350°F. Lightly coat a 12-cup muffin tin with avocado oil spray. In a large bowl, whisk together the dry ingredients - flour, coconut sugar, protein powder, cinnamon, baking powder, baking soda, and salt.
Step 2: In another bowl, mix the wet ingredients - melted coconut oil, cinnamon applesauce, Greek yogurt, maple syrup, eggs, and vanilla, until smooth.
Step 3: Pour the dry ingredients into the wet mixture and stir gently until combined. Do not over mix; this helps keep the muffins light and fluffy.
Step 4: Fold in the diced apples.
Step 5: Divide the batter evenly between the muffin cups, filling nearly to the top. Sprinkle each with a little coconut sugar for a sweet crust.
Step 6: Bake for 22-24 minutes, until the tops are golden and a toothpick inserted in the center comes out clean. Let the muffins cool for 20-30 minutes before eating. Enjoy!
Recipe & Storage Tips
- Don't overmix. Stir only until the flour disappears; protein powder can toughen muffins if overworked.
- Choose your protein wisely. Whey protein yields lighter results, while plant-based powders add density. Avoid "meal replacement" blends with gums or thickeners.
- Keep it moist. Applesauce and Greek yogurt are the secret to soft, bakery-style muffins.
- Storage & Freezer Tips: Store in an airtight container for up to 4 days at room temperature, a week in the fridge, or freeze up to 3 months - perfect for meal prep snacks!
Looking for an indulgent brunch pairing? Try my Hawaiian Roll Cinnamon Rolls!
Recipe FAQs
Yes! Wrap individually and freeze for up to three months. Reheat in the microwave for 30 seconds for a warm, just-baked taste.
Unflavored or vanilla protein powders made for baking are ideal. I love clean whey or pea-protein options that don't add grit.
Yes - swap ¼ cup of flour for quick oats to make oatmeal protein muffins with extra chew.
These gluten-free apple cinnamon protein muffins are your answer to a nourishing fall breakfast that's easy to prep, freezer-friendly, and packed with flavor. Whether you bake them for meal prep, kids' lunches, or a weekend brunch, they'll quickly become a staple in your kitchen.
And don't miss my Gluten-Free Muffins with Dairy-Free Cream Cheese Frosting for another reader-favorite treat!
More Muffin Recipes You'll Love
Apple Cinnamon Protein Muffins (Gluten-Free!)
Equipment
Ingredients
- ¼ cup coconut oil, measured after melting
- ½ cup cinnamon applesauce
- ½ cup plain fat-free Greek yogurt
- 2 tbsp maple syrup
- 2 eggs
- 1 tsp vanilla
- 2 cups gluten free 1:1 flour, I like King Arthur Baking brand
- ½ cup coconut sugar
- ½ cup vanilla protein powder, use code MARY10 for a discount
- 2 tsp cinnamon
- 1 tsp baking powder
- 1 tsp baking soda
- ½ tsp salt
- 1.5 cups finely diced apple, ¼-1/2 inch pieces. About 1 large apple, peeled and cored.
Instructions
- Preheat oven to 350. Spray a muffin tin with avocado oil spray.
- Combine wet ingredients in a large bowl (melted coconut oil, applesauce, yogurt, maple syrup, egg, and vanilla) and mix to combine.
- Add dry ingredients (flour, sugar, protein powder, cinnamon, baking powder, baking soda, and salt) to another bowl and mix to combine.
- Add the dry ingredients into the wet ingredients and stir, then gently fold in the diced apples.
- Divide the mixture evenly between the 12 cups, filling almost to the top. Sprinkle with a little more coconut sugar.
- Bake for 22-24 minutes or until the tops have risen and set.
- Let the muffins cool for 20-30 minutes before enjoying!
Notes
- Don't overmix. Stir only until the flour disappears; protein powder can toughen muffins if overworked.
- Choose your protein wisely. Whey protein yields lighter results, while plant-based powders add density. Avoid "meal replacement" blends with gums or thickeners.
- Keep it moist. Applesauce and Greek yogurt are the secret to soft, bakery-style muffins.
- Storage & Freezer Tips: Store in an airtight container for up to 4 days at room temperature, a week in the fridge, or freeze up to 3 months - perfect for meal prep snacks!
Nutrition
All nutrition facts are an estimate and automatically calculated. While I fact check them using My Fitness Pal, please note that they may not always be 100% accurate and depend on ingredients used. Weigh your total and divide by the number of servings for the most accurate grams per serving size.
Need measurements of the ingredients cannot find it in recipe for the apple protein muffins???
These were delicious! I haven’t baked with protein powder so I wasn’t sure how they would turn out. They were moist and flavorful!
Would coconut yogurt work for dairy free?
I made these fort Bible Study today and my friends went crazy over them. The best gluten- free, protein-packed muffins we’ve had. So tasty and super easy to make. Thanks!