Protein Apple Cinnamon Muffins

Give us a share 💪

If you loved our Protein Blueberry Muffins with Brown Sugar Topping, we have another surprise for you — Protein Apple Cinnamon Muffins!

These muffins are different from your average muffin. Oh no, they’re a quirky twist on a classic. They’re also packed with protein to give you the power to take on the day, one delicious bite at a time.

Don’t let the protein fool you — these muffins are still sweet and delicious, thanks to the juicy apples and warm cinnamon that dance on your tongue with every bite.

And let’s not forget about how easy these muffins are to make. Even if you’re a kitchen newbie, these muffins are foolproof. Just follow the recipe, and in no time, you’ll be chowing down on a muffin that’s so tasty you’ll forget it’s healthy too!

How to Make Protein Apple Cinnamon Muffins

For the best protein muffins, you need to put a little extra care and attention into them, but I promise you, it’ll be worth it. Follow the recipe below and reference the video if you want to see all the steps in action. And for more in depth information on each ingredient, substitutions, variations, expert tips, and more, reference the full post after the recipe card.

Important Notice About Measurements

While every effort has been made to make sure the US / volumetric measurements are generally accurate, We do not recommend using them. There is no guarantee your specific ingredients or your specific scooping technique will measure the same as ours. For the best results, especially with baking recipes such as this one, use a food scale and measure by weight.

Protein Apple Cinnamon Muffins

These protein apple cinnamon muffins are ridiculously moist and flavorful. Actually high protein, but you'd never know it. Filled with sweet apples and cinnamon, they are huge, satisfying, and perfectly balanced. Have one, two, or three for breakfast and you're good to go. Inspired by Mike Bakes NYC Apple Cinnamon Muffins
Course Breakfast, Dessert
Cuisine American
Servings 12 muffins
Calories 201 kcal


Muffins – Wet Ingredients

  • 98 g allulose granulated
  • 60 g butter softened, room temp
  • 8 g molasses
  • 124 g egg room temp
  • 224 g fat-free Greek yogurt room temp
  • 128 g applesauce room temp
  • 13 g vanilla extract

Muffins – Dry Ingredients

  • 160 g all-purpose flour
  • 80 g unflavored whey protein
  • 80 g collagen peptides
  • 80 g soluble corn fiber
  • 8 g xanthan gum
  • 8 g salt
  • 13 g baking powder
  • 4 g baking soda
  • 7 g stevia powder
  • 8 g cinnamon ground
  • 200 g apples

Crumble Topping

  • 30 g allulose granulated
  • 12 g unflavored whey protein
  • 20 g rolled oats either quick or old fashioned
  • 1 g salt coarse sea salt
  • 1.2 g cinnamon ground
  • 6 g butter
  • 4 g molasses
  • 7 g egg whites


  • 38 g Neufchatel cream cheese (aka 1/3 fat cream cheese)
  • 38 g allulose powdered
  • 12 g casein protein unflavored or vanilla
  • 1 g vanilla extract alcohol-free (omit if using vanilla casein)
  • 1 g stevia powder
  • 30 g water


  • Add butter, allulose, and molasses to a bowl and beat on high speed with a hand mixer or stand mixer until smooth and creamy. Make sure to scrape down the sides as necessary to get it all incorporated.
  • Add remaining wet ingredients and beat on high until fully combined.
  • In a separate bowl, sift together all dry ingredients then mix with a whisk. Add dry ingredients to wet ingredients and mix on low speed or by hand until just combined. Cover and place in fridge for ~30 minutes.
  • Preheat oven to 425F / 220C, making sure oven rack is in the center position or one position lower than center (not too close to the top).
  • Add all crumble topping ingredients to a small mixing bowl and work them together with a pastry cutter or fork. (You can also use your fingers to help break up any clumps)
  • Add all frosting ingredients to a small bowl and mix with a hand mixer until very smooth. Cover and set aside.
  • Chop apples into small pieces (final amount should match what is in recipe), toss them in a small amount of flour, then fold them into the batter.
  • Fill muffin pan with liners then scoop ~90g of batter into each. (If you followed all measurements correctly, this will make 12 muffins, allowing for a little leftover on spoons and bowl).
  • Place into oven on center rack and bake for 5 minutes. Then reduce the temperature to 325F / 160C and bake for an additional 20-23 minutes or until a toothpick comes out clean. Remove from oven and let cool for 5 minutes before removing from pan and placing on a wire rack.
  • Drizzle with frosting (add a little more water if necessary) and and let the muffins continue to cool while the frosting firms up a bit.
Keyword Apple, Cinnamon, Muffins

Why This Recipe Is Great

Quick and Easy

You’ll only need one bowl and a muffin pan for this recipe, making it a hassle-free bake! This means you have fewer dishes to wash and more time to enjoy your muffins!

Bursting Apple Flavors

Applesauce plus apple muffins? We promise we’re not apple addicts! The applesauce is a great stand-in for oil to keep the muffins moist without any added saturated fats. Meanwhile, the chopped apples offer a juicy burst of flavor in every bite. Trust us — you won’t get enough of these muffins!

Perfectly Macro Friendly

With protein powder and other alternatives, our recipe is healthier than any other apple cinnamon muffins out there. You’ll get the macronutrients you need and without missing out on any flavor or texture!

Great to Make in Bulk

Our recipe can be done in bulk and frozen for later, which is perfect for those who love meal prepping. You can easily double or triple the recipe and have muffins on hand for the week. They’re perfect for quick breakfasts or snacks on the go.

Crumble Topping with A Punch

These muffins have a crumble topping that’s light in calories but with great benefits. It adds a delicious crunch and texture and is the perfect finishing touch to these already amazing muffins.

Muffin Ingredients

This protein apple cinnamon muffin recipe calls for several ingredients that work together to create a delicious and nutritious muffin. Let’s break it down ingredient by ingredient, and we’ll give you the lowdown on why they’re important.

All-Purpose Flour

All-purpose flour provides structure and texture to baked goods. It contains gluten, which helps to bind the ingredients together and create a light and fluffy texture while keeping that classic muffin taste. Think of it as the backbone of the muffins.

Whey Protein Powder

Whey protein powder is a highly concentrated form of protein derived from milk. It provides a source of high-quality protein to the recipe. Think of that gym buddy you never knew you needed — it helps build and repair muscles while keeping you full and satisfied.

Greek Yogurt

Greek yogurt is a creamy and tangy dairy product high in calcium and protein, making these muffins moist and rich in flavor. Not to mention, it’s also low on calories.

Stevia Powder and Granulated Allulose

Stevia powder and granulated allulose are the sweethearts of the recipe. They provide natural sweetness without adding any extra calories or sugar. The combo makes it easier for the muffins to hold moisture, critical to the baked goods’ browning, taste, and shelf-life.

Unsweetened Apple Sauce

Aside from being a great alternative to oil and butter, unsweetened apple sauce is also a low-calorie ingredient that adds natural sweetness to the muffins. This sneaky ingredient adds a ton of apple flavor and moisture without you even realizing it!

Collagen Protein

Collagen protein is another source of protein that doesn’t change the texture or flavor of the muffins too much. Collagen is often used as a supplement to support skin elasticity, joint health, and other benefits to health and wellness, so it’s good to add to our diet.

Corn Fiber

Corn fiber is a dietary fiber that adds bulk to the muffins, which helps create a satisfying texture and promote satiety without the grittiness.

Xanthan Gum

If the all-purpose flour is the muffin’s backbone, think of the xanthan gun as the glue that holds the muffins in place. It’s a thickener and stabilizer derived from fermented sugar and is critical for structure. It assists in binding ingredients together to create a cohesive texture in the muffins.


Molasses is a thick, dark syrup made from sugar cane or sugar beet juice. We’re using this to give a bit of brown sugar flavor (without adding the brown sugar), as it provides a rich flavor and color to the muffins. It also has more minerals and vitamins than other types of sugars.


Butter is a type of fat that adds richness and flavor. We use just enough butter to make the muffins moist and buttery without adding too many extra calories. Here’s a tip: You can reduce the butter and replace it with more applesauce.

Apples and Cinnamon

Apples and cinnamon are classic flavors that pair well together. They add natural sweetness, warm spice to the muffins, and a pleasant texture from the small chunks of apple throughout.

We prefer to dice the apples up for this recipe, but you can chop them in whatever size you prefer. You can even shred them or use a food processor if you want.

Crumble Topping Ingredients

Granulated Allulose

Granulated allulose is a sweetener that is low in calories and has a taste and texture similar to sugar. It replaces sugar in the crumble topping as it gives sweetness without adding too many calories. Plus, it doesn’t raise blood sugar levels as much as regular sugar, making it a good option for those watching their sugar intake.


Molasses has a rich, smoky, caramel-like flavor that adds depth to the crumble topping. Combined with allulose or other granulated sweeteners, it makes an excellent brown sugar substitute.

Unflavored Whey Protein

Unflavored whey protein is excellent for sneaking extra protein in the crumble topping without too much altering the flavor or texture. Protein is vital for building and repairing muscle tissue, so it’s a good idea to include it in snacks and meals whenever possible.

Rolled Oats

Rolled oats are perfect for traditional oat crumble with their trademark crunch and texture. They are also a good source of fiber and protein that make you feel full longer.


Butter is a classic ingredient in crumbles because the topping needs to be oiled to crisp up. But it’s important to use it in moderation since it is high in calories and saturated fat.

Egg Whites

Egg whites help the topping clump into crumble pieces. They are also a good source of protein, which is always a bonus!

Frosting Ingredients

Neufchatel Cheese

This is a type of cream cheese that is lower in fat and calories (versus traditional cream cheese.) Don’t worry; it tastes just like the full-fat version and provides that creamy mouthfeel texture, and is a great choice for cream cheese-flavored frosting.

Powdered Allulose

Powdered allulose is a low-calorie sweetener similar in taste and texture to powdered sugar. It’s a great alternative to traditional powdered sugar because it doesn’t raise blood sugar levels as much and helps whip and firm up the frosting.

Casein Protein

Casein protein is another source of protein that doesn’t change the frosting’s texture or taste. It also thickens the frosting. You can try a flavored protein here if you want.

Toppings and Customizations

Here are a few options for your customized muffin recipes:

Classic Streusel

Stick with the classic butter, flour, and brown sugar topping.

Greek Yogurt Frosting

If you’re looking for a healthier option, try using Greek yogurt as the base for your frosting. Mix Greek yogurt, powdered sweetener, and a bit of vanilla extract until smooth and creamy.

Whipped Coconut Cream Frosting

Try whipping up some coconut cream with powdered sweetener and vanilla extract for a dairy-free option. This will create a light and fluffy frosting perfect for the apple muffins.

Cinnamon Frosting

If you want to enhance the cinnamon flavor of the muffins, create a simple cinnamon frosting. Mix together powdered sweetener, cinnamon, and softened butter until smooth and creamy.

Pears Instead of Apples

Pears can easily substitute apples because of their similar texture and sweetness. Cinnamon is a spice that pairs well with both apples and pears, so you can keep that the same. 

However, you may want to adjust the amount of cinnamon depending on the sweetness of your pears. You can also experiment with adding other spices like nutmeg, allspice, or ginger to complement the flavor of the pears.

Chopped Nuts

Add some crunch and flavor to the muffins by topping them with chopped nuts like peanuts, pecans, or walnuts.

Caramel Sauce

Add a sweet and sticky caramel sauce to the apple muffins for an indulgent treat.

Maple Syrup

Whip up a quick maple glaze made from powdered sweetener, maple syrup, and milk. Add salt if you want, then drizzle it over the healthy apple muffins for a delicious and sweet finish.

Custom Mix-ins

You could also customize the apple muffins by adding your favorite mix-ins, like raisinsor chocolate chips. Get creative and experiment with different flavors and textures!

Everything Almond: Almond Flour, Almond Milk, Almond Butter

Go all out and use almond flour instead of all-purpose for mild sweetness that’s great for savory muffins. Almond flour also extends baked goods’ shelf life. Note that you may need more eggs and xanthan gum for binding, though.

You can also add almond milk for a nuttier taste. However, the muffin may be slightly drier unless you under-bake the goodies.

Almond butter is popular in vegan baking. In this case, you can use almond butter and its high (healthy) fat content to substitute butter. It’s also tastier.

Top Hot Muffins with Honey Butter or Jam

Honey butter is a simple yet delicious spread that adds sweetness and richness to the muffins. To make honey butter, mix softened butter and honey until smooth and creamy.

Jam is another great option for adding sweetness and flavor to your muffins. You could use any type of jam you like — strawberry, raspberry, blueberry, or even apple! Once your muffins are baked and cooled, spread a layer of jam onto each.

You can also combine honey butter and jam for a truly extravagant treat! Simply spread a layer of honey butter onto your muffins, then top with a dollop of your favorite jam. This combination of sweet and rich flavors is sure to be a crowd-pleaser.

Quick Oats Instead of Rolled Oats

If you only have quick-cooking oats in your kitchen, you can still use them for your crumble. Although the oats will take less time to cook, you will want to lessen your butter.

You may also want to try instant oats that are finer milled than quick oats. This is okay, but bear in mind that they don’t have much of the crunch we’re after.

Expert Tips for Apple Cinnamon Protein Muffins

Don’t Overmix the Batter

Overmixing the batter can result in tough, dense muffins. Mix the ingredients together until just combined, and avoid stirring the batter too much.

Use Room-Temperature Ingredients

Using room-temperature ingredients, such as eggs and butter, can help ensure the ingredients mix together more easily and create a smoother batter.

Measure Ingredients Carefully

It’s important to measure out your ingredients accurately, especially when it comes to the dry ingredients. Too much flour or protein powder can result in dry, crumbly muffins.

Use Fresh Apples

Fresh, ripe apples will add the most flavor and moisture to your muffins. Chop the apples into small, even pieces so that they bake evenly.

Adjust Spices to Taste

The amount of cinnamon and other spices you use varies depending on your personal taste preferences. Adjust the spices as needed to achieve your desired level of flavor.

Let Muffins Cool Completely Before Topping

Letting your muffins cool completely before adding toppings or frosting is crucial. This will prevent the toppings from melting or sliding off the muffins.

Bulk Prepping and Storage Tips for Healthy Apple Muffins

Make a Large Batch

Instead of making just a few muffins at a time, consider making a larger batch all at once. This will save you time and effort in the long run, and you can store the extra muffins for later.

Use Muffin Liners

Muffin liners can make removing the muffins from the pan easier and prevent sticking. This is especially helpful if you plan to freeze the muffins.

Store in an Airtight Container

Once the muffins have cooled, store them in an airtight container to help keep them fresh. You can also add a piece of bread to the container to help absorb any excess moisture and keep the muffins from getting too soggy.

Freeze Individual Muffins

Consider freezing the muffins individually if you plan to store them in the freezer. Place each muffin in a small plastic bag or wrap them in plastic wrap so they don’t stick or get freezer burn, then store them all together in a larger freezer bag.

Label and Date the Muffins

To make it easier to track when your muffins were made and when they need to be used, label and date them before storing. This is to avoid food waste and ensure that you’re always eating fresh muffins.

Thaw Muffins Overnight

When you’re ready to eat, thaw the frozen muffin in the refrigerator overnight or at room temperature for an hour. You can also reheat the muffin in the microwave for a few seconds to warm it up before eating.

Frequently Asked Questions

Can these muffins be made gluten-free?

Yes, these muffins can be made gluten-free by substituting the all-purpose flour with a gluten-free blend. Additionally, it’s important to ensure that any other ingredients used, such as oats or corn fiber, are also certified gluten-free.

How much protein is in apple cinnamon muffins?

The amount of protein in apple cinnamon muffins will vary depending on the specific recipe and ingredients used. However, a typical apple cinnamon muffin may contain around 3 to 5 grams of protein per serving.

Our healthy apple cinnamon muffins recipe has 19 grams of protein.

How many calories are in an apple and cinnamon muffin?

A regular apple and cinnamon muffin can contain anywhere from 300-500 calories, depending on the size and ingredients used. Most store-bought muffins tend to be on the higher end of this range, as they often contain added sugars and fats.

Our healthy apple cinnamon muffins are only 201 calories each.

What nutrition is in apple cinnamon muffins?

Regular apple cinnamon muffins may contain high amounts of refined sugars and unhealthy fats while lacking significant protein and fiber. On the other hand, our recipe for apple cinnamon protein muffins includes nutritious ingredients like whey protein powder, Greek yogurt, and unsweetened applesauce, providing more protein and fiber with less added sugars and unhealthy fats.

Overall, our recipe is a healthier alternative to regular apple cinnamon muffins.

How do you add protein to boxed muffin mix?

To add protein to boxed muffin mix, you can use ingredients like protein powder, Greek yogurt, or nut butter in place of some of the traditional ingredients like flour or oil. Simply mix the additional protein source into the batter according to the package instructions, or use a recipe that specifically calls for protein-rich ingredients. This can increase the overall protein content of the muffins, making them a healthier and more satisfying snack or breakfast option.


To wrap it up, apple cinnamon protein muffins are like a high-five from your taste buds to your health goals. They’re packed with protein to energize and satisfy throughout the day. Plus, these apple protein muffins are loaded with the sweet and spicy flavors of apples and cinnamon — a definite party in your mouth!

So whether you’re looking for a grab-and-go breakfast or a midday snack, these muffins are the perfect way to satisfy your cravings and fuel your body. Don’t settle for boring old muffins — give our recipe for protein apple cinnamon muffins a try and indulge in a healthy, delicious treat that will make you say “yum” with every bite!

About FitHackr

Building a collection of high protein, macro friendly recipes so you can get and stay fit while eating your favorite foods.

Developing, testing, and shooting new recipes every week. Follow the social media pages below for new recipes as they’re released.