Apple Cinnamon Protein Muffins

The only thing better than fall-inspired muffins is Apple Cinnamon Protein Muffins! Made with real apple chunks, fragrant cinnamon, and hidden protein powder, these healthy treats are perfect for a satiating grab-and-go snack or a protein-rich dessert.

This cozy apple cinnamon protein muffin recipe has all the fall flavors you love to celebrate the season, and it provides the energy you need to fuel your day – whether wandering through a pumpkin patch, tackling your to-do list, or wrangling kiddos. P.S. Kids love them too!

The tender muffin texture is riddled with chunks of fresh juicy apple and the perfect amount of warming cinnamon. Greek yogurt and apple sauce add a delicious moistness while a sprinkle of rolled oats adds a hearty topping. Protein powder makes this tasty snack a sneaky good source of protein while whole wheat pastry flour adds fiber, vitamins, and minerals. Brown sugar and granulated sugar add a delicious subtle sweetness that will satisfy your sweet tooth without overpowering your taste buds. 

These healthy apple cinnamon muffins are incredibly easy to prepare in less than 30 minutes! Whip up a batch to enjoy throughout the week. Add them to school lunches or enjoy them for breakfast or a midday snack with a warm cup of coffee or tea. For more healthy muffin recipes, try my Pumpkin Protein Muffins, Healthy Lemon Zucchini Muffins, or Banana Carrot Muffins. 

What do apple cinnamon protein muffins taste like? 

Each bite of these healthy apple muffins melts in your mouth with the perfect combination of cozy, sweet, and satisfying flavors and textures. The moist, cake-like mouthfeel is indulgent, fresh apple chunks add tender chewy pockets of festive flavor, and spicy cinnamon provides a comforting warmth. There is a lovely natural sweetness from the apple pieces, applesauce, and a hint of brown and granulated sugars. 

Whole wheat pastry flour and protein powder add a hearty element while creamy Greek yogurt keeps the high-protein muffins extra moist and tender. The combination of wholesome ingredients gives these muffins a filling, nourishing quality without feeling heavy. A rolled oat streusel-like topping adds a pleasant crunch on top with a rustic, homemade feel.  

Why You Will Love Apple Protein Muffins

• Nutritious – These healthy protein muffins are a balanced treat packed with protein and healthy carbohydrates and low in fat. The wholesome ingredients will keep you full and nourished, giving you energy throughout the day. 
• Budget-Friendly – The simple ingredients cost less than $5 to make one dozen muffins, making this an affordable healthy eating option! 
• Easy Prep – This protein muffins recipe comes together quickly with just 10 minutes of easy hands-on preparation, then they bake in the oven for less than 20 minutes. You’ll have ready-to-eat muffins in less than 30 minutes!
• Fall Flavors – Made with fresh apple pieces, warming cinnamon, and a touch of brown sugar, these protein apple muffins capture the best of fall in every bite.

Ingredients

• Whole Wheat Pastry Flour – Gives the muffins a tender yet sturdy texture and adds fiber and nutrients. 
• Protein Powder – Choose your favorite brand of plain or vanilla-flavored protein powder to add a hint of vanilla sweetness and a boost of satiating protein.
• Baking Powder & Baking Soda – Serve as leveaning agents to help the muffins rise in the oven and maintain a fluffy texture. 
• Granulated Sugar – Adds a subtle sweetness and helps the muffin achieve a light crumb texture. 
• Brown Sugar – Use light or dark brown sugar to add a caramel-like flavor and extra moisture to the muffins; choose light for a milder sweetness or dark brown sugar for a stronger molasses flavor. Always pack the sugar tightly when measuring it.
• Greek Yogurt – Adds moisture and tenderness and provides added protein. Use a plain, unsweetened Greek yogurt to avoid excess sugars and flavors, and opt for a full-fat option for moist muffins.
• Applesauce – Unsweetened applesauce enhances the natural sweetness and apple flavor while keeping the muffins extra moist and reducing the need for added fats.  
• Eggs – Use large eggs to provide a sturdy structure that holds the muffins together and contributes to a tender crumb. 
• Chopped Apples – Fresh apple pieces add juicy, fruity flavor in each bite. Use Granny Smith for a tart contrast to the muffins’ sweetness or Honeycrisp for a sweeter, juicier bite. 
• Old Fashioned Rolled Oats – Used as an optional wholesome garnish to add a hearty crunch to the muffins, providing a texture contrast and additional whole grains.

Substitutions

• Whole Wheat Pastry Flour – Swap for a 1:1 mixture of all-purpose and whole wheat flour for a similar texture, albeit fewer whole grains.
• Protein Powder – Use unflavored or vanilla collagen peptides. For vegan protein powder muffins, use a plant-based powder.
• Granulated & Brown Sugar – Substitute raw cane sugar or coconut sugar for less processed sugar option. 
• Greek Yogurt – Plain, unsweetened regular yogurt or sour cream maintains the creaminess and slightly tangy flavor. Or, swap with coconut yogurt or another dairy-free yogurt. 
• Applesauce – Swap in pumpkin puree for a different fall flavor or mashed banana for a sweeter alternative.  
• Eggs – Make a vegan egg substitute by combining 1 tablespoon of ground flax or chia meal with 2.5 tablespoons of water; let it gel for at least 10 minutes before adding. Or add ¼ cup of applesauce (in addition to the other applesauce in the recipe). 
• Chopped Apples – Use another firm fall fruit, like chopped fresh pears or persimmons for similar moisture and texture. 
• Old Fashioned Rolled Oats – Quick oats provide a similar topping texture. Or, omit them altogether if you prefer the muffins without.

Instructions

Below are the simple, wholesome ingredients you need to make fall-inspired high-protein muffin recipes: 

• Step 1: Preheat the oven to 350°F and line a 12-count muffin tin with muffin liners. 
• Step 2: Combine the dry ingredients in a medium bowl–the flour, protein powder, cinnamon, baking powder, baking soda, and salt–until well combined. Set aside. 
• Step 3: Combine the wet ingredients in a separate bowl–the Greek yogurt, applesauce, granulated and brown sugars, eggs, and vanilla. Whisk until well combined and no clumps of yogurt remain. 
• Step 4: Combine the dry and wet ingredients, stirring until just combined. Then fold in the chopped apples. 
• Step 5: Divide the batter evenly between the 12 muffin cups. Evenly sprinkle the tops of the muffins with rolled oats, then bake for 16-18 minutes or until a toothpick inserted in the center comes out clean. Allow to cool completely before serving.

Recipe Tips

• Use a quality protein powder. Choose a good protein powder that you already know you enjoy–some can seem chalky or add an odd taste depending on your preference. Stick with an unflavored variety for a tasteless addition, or use a vanilla-flavored protein to enhance the other muffin flavors. 
• Pick your favorite apples. High protein apple recipes work with any type of apple, so choose your favorite–Granny Smith for a tarter flavor or Honeycrisp or Fuji for a sweet-tart flavor. 
• Don’t overmix. For the most tender muffins, do not overmix the batter. Mix the wet and dry ingredients until combined, then gently fold in the apple pieces. 
• Optional apple texture. Leave the apple peels intact for added texture, or peel them before chopping to help them melt into the crumb. 
• Add mix-ins. Customize your muffins by adding ¼-½ cups of chopped nuts, dried fruit like raisins, cranberries, chopped dates, chocolate chips, or ¼ cup of shredded coconut. 
• Test for doneness. Avoid overbaking by checking on the muffins 1-2 minutes before the end of the cooking time. If a toothpick inserted into the center of one muffin comes out with moist crumbs, they are perfectly baked! They will continue to cook slightly as they cool.

Serving Suggestions

Enjoy a protein muffin for a cozy breakfast with a dollop of Greek yogurt and honey drizzle, pack them in school lunches, or munch on them throughout the week as a healthy snack. They are also delicious paired with one of our favorite tasty seasonal drink recipes below as a healthy dessert or mid-day treat: 

• Homemade Pumpkin Spice Latte
• Pecan Crunch Oatmilk Latte
• Healthy Dairy-Free Hot Chocolate

Storage Directions

• Storage: Cool the muffins completely before transferring them to an airtight container lined with a paper towel to absorb any moisture, and store them at room temperature for up to 3 days.
• Refrigeration: Store cooled muffins in an airtight container in the refrigerator for up to 1 week. 
• Freezing: Place cooled muffins in an airtight freezer-safe container for up to 3 months. Defrost them at room temperature for 30 minutes – 1 hour or overnight in the fridge.
• Reheating: Warm refrigerated muffins in the microwave for 10-15 seconds or in the oven at 300ºF for 5-7 minutes to refresh the texture.

Nutritional Info

These healthy protein muffins are as nutritious as they are flavorful, making them the perfect wholesome snack or breakfast option. Each muffin contains a moderate 151 calories and provides a sustainable energy source with 8 grams of protein and 27 grams of complex carbohydrates per serving. Many carbohydrates are whole grains from whole wheat pastry flour and oats, but a few come from sweeteners that add satisfaction and flavor. Each muffin contains 3 grams of dietary fiber to help stabilize blood sugar and aid in digestive health. 

The muffins are low in fat, with just 2 grams of total per serving, which helps keep them light while still satisfying. The sodium content is on the higher end, with 276mg per serving, mostly due to the baking powder, which is an essential ingredient that helps the muffins rise when baking. However, you can help reduce the sodium content if desired by choosing a low-sodium protein powder or reducing the amount of salt.

Total nutritional content per serving is:

• Calories: 151 calories
• Total Fat: 2 grams
• Protein: 8 grams
• Sodium: 276 mg
• Carbohydrates: 27 grams
• Fiber: 3 grams

*This nutritional information is an estimate and calculated based on the ingredients used to create the recipe. The nutritional value of your ingredients may differ slightly. Furthermore, this food is not intended to prevent, diagnose, cure, or treat any disease.

Pricing Info

This is what I personally paid to make this recipe:

• 1 ¼ cups whole wheat pastry flour: $0.33
• ½ cup protein powder: $1.76
• 1 tbsp cinnamon: $0.06
• 1 tsp baking powder: $0.04
• ½ tsp baking soda: $0.01
• ¼ tsp salt: $0.01
• ½ cup granulated sugar: $0.17
• ½ cup plain Greek yogurt: $0.50
• ¼ cup unsweetened applesauce: $0.14
• ¼ cup brown sugar: $0.12
• 2 large eggs: $0.90
• 1 tsp vanilla extract: $0.04
• 1 cup finely chopped apples: $0.45
• 2 tbsp old fashioned rolled oats: $.03

The total comes out to be around $4.56 or roughly $0.38 per muffin!

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Recipe

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5 from 4 votes

Apple Cinnamon Protein Muffins

These fall-inspired Apple Cinnamon Protein Muffins are the perfect healthy snack or breakfast option, made with fresh apple chunks, whole grains, fragrant cinnamon, and plenty of protein. Make this easy recipe in less than 30 minutes!

Prep Time10 minutes mins

Cook Time16 minutes mins

Total Time26 minutes mins

Course: Breakfast

Cuisine: American

Servings: 12 muffins

Calories: 151kcal

Author: Megan Byrd, RD

Cost: $4.56 or $0.38/muffin

Ingredients

• 1 ¼ cups whole wheat pastry flour
• ½ cup protein powder plain or vanilla
• 1 tbsp cinnamon
• 1 tsp baking powder
• ½ tsp baking soda
• ¼ tsp salt
• ½ cup granulated sugar
• ½ cup plain Greek yogurt
• ¼ cup unsweetened applesauce
• ¼ cup brown sugar packed
• 2 large eggs
• 1 tsp vanilla extract
• 1 cup finely chopped apples
• 2 tbsp old fashioned rolled oats (optional for sprinkling)

Instructions

• Preheat your oven to 350° and line a 12-count muffin tin.
• In a medium bowl, mix together the flour, protein powder, cinnamon, baking powder, baking soda, and salt. Set aside.
• In a separate bowl, whisk together granulated sugar, plain Greek yogurt, applesauce, brown sugar, eggs, and vanilla. Whisk until no clumps of yogurt remain.
• Add the dry ingredients and stir until just combined. Fold in the chopped apples.
• Divide the batter evenly between 12 muffins. Sprinkle rolled oats evenly onto each muffin, then bake for 16-18 minutes or until a toothpick inserted in the center comes out clean. Allow to cool, then serve!

Notes

Storage Directions

• Storage: Allow the muffins to cool completely before transferring them to an airtight container lined with a paper towel to absorb any moisture, and store them at room temperature for up to 3 days.
• Refrigeration: Store cooled muffins in an airtight container in the refrigerator for up to 1 week. 
• Freezing: Wrap individually muffins tightly in plastic wrap or aluminum foil, then place them in an airtight freezer-safe container for up to 3 months.
• Reheating: Warm refrigerated muffins in the microwave for 10-15 seconds or in the oven at 300ºF for 5-7 minutes to refresh the texture. Thaw frozen muffins overnight in the refrigerator before reheating.

Nutrition

Serving: 1muffin | Calories: 151kcal | Carbohydrates: 27g | Protein: 8g | Fat: 2g | Sodium: 276mg | Fiber: 3g

If you end up making this and loving it, take a photo and tag me on Instagram! I’d love to see your versions of my recipes! And feel free to rate it down below in the comment section. I would really appreciate it!

xoxo Megan