Estimated per muffin, including cinnamon topping and excluding the optional glaze.
These Apple Pie Protein Muffins are basically the breakfast version of an apple crumble.
The muffins are loaded with diced apples, topped with more apples and a buttery cinnamon crumble, then finished with a simple cinnamon glaze. I made this batch into 12 larger muffins, and each one comes in around 172 calories with 12.2g of protein before the glaze.
The Greek yogurt keeps the muffins soft, while protein powder bumps up the protein without taking over the recipe. The cinnamon topping is what really gives them that apple pie feel.
Try These Next
If you're looking for other protein muffin recipes from the archive, try these:
- High Protein Cottage Cheese Blueberry Muffins — another fruit-filled breakfast muffin with plenty of protein.
- Raspberry Protein Muffins — a good option when you want something fruity without the fall flavors.
- Pumpkin Protein Muffins — probably the closest match when you want another high-protein muffin for fall.
Apples in the Batter and on Top
There are two things doing most of the work here: using apples in two places and keeping the cinnamon topping separate from the batter.
I fold 1½ cups of diced apples into the muffins, so there are pieces of apple throughout the center.
Then I save another ½ cup for the tops.
That makes a bigger difference than throwing all two cups into the batter. You actually see and taste the apples when you bite into the finished muffin.
The cinnamon crumble goes on last. It stays closer to the top instead of disappearing into the batter, which gives these much more of an apple pie or apple crisp feel.
Why You'll Love These Apple Pie Protein Muffins
- 12g of protein per muffin: Each muffin has about 12.2g before adding the optional glaze.
- Lots of real apple: Two full cups of diced apples go into the batch.
- Big muffins: This makes 12 substantial muffins rather than a tray of tiny protein bites.
- Soft center: Greek yogurt and skim milk keep the batter moist.
- Apple pie topping: The buttery cinnamon crumble and extra apples make these feel much more like dessert than a basic apple muffin.
- Good for meal prep: Bake a dozen at once and keep breakfast or snacks ready for several days.
Key Equipment
12-Cup Muffin Tin: This is a full 12-muffin batch, and the muffins are fairly large. Divide the batter evenly so they bake at roughly the same rate.
Digital Kitchen Scale: I gave the flour and protein powder in grams because those are two ingredients where a little extra can make protein muffins noticeably drier.
Pyrex Mixing Bowl Set: You need one bowl for the wet ingredients, one for the dry mixture, and a small bowl for the cinnamon topping.
Silicone Spatula Set: This is especially useful once the apples go in. Fold them through gently instead of beating the batter.
Pyrex Mixing Bowl Set
Keep the wet ingredients, dry ingredients, and cinnamon topping separate while you prepare the batter.
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Ingredient Notes
Apples: These are the main flavor and also add moisture. Dice them fairly small so every muffin gets plenty of apple without leaving huge wet pockets in the center.
All-Purpose Flour: Regular flour keeps enough structure in the muffins to support all of those apples and the crumble topping.
Greek Yogurt: Plain nonfat Greek yogurt adds protein and moisture without needing oil in the batter.
Skim Milk: The milk loosens the batter and gives the flour and protein powder the moisture they need. Add it alternately with the dry ingredients, as directed in the recipe.
Zero-Calorie Sugar Alternative: I use a cup-for-cup replacement here so the volume is similar to granulated sugar without adding the same calories.
Egg: One egg helps bind everything together and gives the muffins enough structure to rise.
Cinnamon: There is cinnamon in the topping and you can also add it to the glaze. That is what pushes these firmly into apple pie territory.
Butter: The batter itself does not use butter, but the cinnamon topping does. I like putting it where you can actually taste it.
How to Make Apple Pie Protein Muffins
1. Prep the oven and pan: Heat the oven to 350°F and line a 12-cup muffin tin with liners.
Set aside ½ cup of the diced apples. These will go on top instead of into the batter.
2. Make the cinnamon topping: Mix the sugar alternative, flour, melted butter, and cinnamon together in a small bowl.
The mixture should look crumbly rather than like a smooth paste. Set it aside while you make the batter.
3. Mix the wet ingredients: In a large bowl, whisk together the sugar alternative, Greek yogurt, egg, and vanilla until smooth.
You do not need to beat this aggressively. Just get rid of any obvious lumps of yogurt.
4. Combine the dry ingredients: In a separate bowl, mix the flour, protein powder, baking soda, baking powder, and salt.
Breaking up the protein powder now helps prevent dry pockets later.
Pro Tip: If you're weighing ingredients, this is where the Digital Kitchen Scale matters most. An extra scoop of flour or protein powder can turn a soft muffin into a dry one.
5. Build the batter: Add the dry ingredients to the yogurt mixture alternately with the skim milk.
Mix only until everything comes together.
Do not keep stirring once the flour disappears.
Pro Tip: Muffin batter does not need to be perfectly smooth. A few small lumps are better than overmixing it.
6. Fold in the apples: Add 1½ cups of diced apples and gently fold them through with a Silicone Spatula.
Try to distribute them evenly so every muffin gets plenty of apple.
7. Fill and top: Divide the batter evenly among all 12 muffin cups.
Leave enough room for the muffins to rise.
Add the reserved ½ cup of apples across the tops, then sprinkle the cinnamon crumble over each muffin.
8. Bake: Bake at 350°F and start checking them around 25 minutes.
Bake for 25–30 minutes, using the center of the muffins as your guide.
A toothpick should come out without wet batter attached.
Pro Tip: A little moisture from an apple is fine. What you do not want is raw muffin batter on the toothpick.
9. Cool completely: Let the muffins cool before adding the glaze.
The tops are delicate while warm, especially with the apples and crumble sitting on them.
10. Glaze: Mix powdered sugar, milk, and cinnamon until you have a drizzleable glaze.
Drizzle it across the cooled muffins in a zigzag pattern.
Since I did not measure the glaze when I made these, I would add the milk a very small amount at a time. You can always thin it more.
Expert Tips
Dice the Apples Small
Big apple chunks sound good, but they can leave wet pockets inside the muffin.
Small dice distributes the fruit better and gives you apple in almost every bite.
Do Not Overmix the Batter
Once the flour and protein powder go in, mix only until everything is combined.
Too much stirring can make muffins tougher and denser.
Keep the Reserved Apples for the Top
Do not accidentally fold all two cups into the batter.
That ½ cup on top is part of what makes the finished muffins look and taste more like apple pie.
Watch the Center, Not Just the Topping
The cinnamon crumble can look finished before the middle of a large muffin is actually baked.
Check the center around 25 minutes and keep going if there is still wet batter.
Cool Before Glazing
Warm muffins will melt the glaze almost immediately.
If you want that visible white cinnamon zigzag across the top, let them cool first.
Troubleshooting & Frequently Asked Questions
Why are my protein muffins dry?
The two biggest causes are too much dry ingredient or too much baking time.
Protein powder already absorbs quite a bit of moisture. Measuring the flour and protein powder by weight helps.
Also, start checking at 25 minutes instead of automatically baking to the far end of the range.
Why did my apple muffins turn gummy in the center?
The apples may have been cut too large, or the muffins may simply need more time.
These contain a lot of fresh fruit. Large pieces release moisture as they bake.
Dice the apples fairly small and make sure the middle has set before pulling the tray.
Why are my muffins dense?
Overmixing is a common reason.
Once you combine flour with wet ingredients, keep the mixing gentle and stop as soon as the batter comes together.
Can I make these without protein powder?
Not as a straight one-for-one omission.
The protein powder is part of the dry ingredient balance in this recipe. Removing 98g would significantly change the batter.
Can I use a different kind of apple?
Yes.
I would use an apple that holds its shape fairly well when baked. You can also mix sweeter and more tart apples if that is what you have.
Can I skip the cinnamon topping?
You can, but it changes the recipe quite a bit.
The muffins themselves will still bake, but that crumble is a big part of the apple pie flavor and texture.
How do I know the muffins are done?
Start checking at 25 minutes.
The tops should be set, and a toothpick inserted into the center should come out without wet batter.
If you hit a piece of apple, move the toothpick and check another spot.
Variations and Substitutions
These are optional ideas, not tested versions of this recipe. For the result and nutrition described here, follow the recipe card. Ingredient changes can affect texture and macros.
| Component | Swap Options |
|---|---|
| Apples | Use your favorite firm baking apple or a mix of sweet and tart apples |
| Skim milk | Another milk can work, but nutrition and moisture may vary |
| Greek yogurt | Another thick plain Greek yogurt should work; higher-fat yogurt will change macros |
| Cinnamon | Apple pie spice can give the topping a stronger fall flavor |
| Sugar alternative | Use another cup-for-cup granulated sweetener designed for baking |
| Glaze | Skip it completely or make a thicker icing with less milk |
| Cinnamon topping | Add chopped pecans or walnuts if you want more crunch |
Storage & Reheating
Let the muffins cool completely before storing them.
Keep them in an airtight container in the refrigerator for up to 5 days.
Because these contain a lot of fresh apple and Greek yogurt, I prefer refrigerating them rather than leaving them on the counter for several days.
For a warm muffin, microwave one for about 15–20 seconds.
If the muffin is glazed, keep in mind the glaze will soften when reheated.
You can also freeze the unglazed muffins. Wrap them individually and place them in a freezer-safe container.
Thaw overnight in the refrigerator or microwave briefly from frozen.
If you plan to freeze them, I would wait and add the glaze after thawing.
Nutrition
The estimated nutrition for this recipe is based on 12 muffins and includes the full cinnamon topping.
The unmeasured glaze is not included.
Per Muffin Before Glaze
- Calories: 172
- Protein: 12.2g
- Carbohydrates: 21.1g
- Fat: 4.1g
The calculation also excludes carbohydrate values from the zero-calorie sugar alternative and assumes the protein powder contributes 0g fat.
Exact nutrition will vary by protein powder, yogurt, milk, apples, sweetener, and the amount of glaze you add.
You Might Also Like
If you're trying to keep high-protein muffins in your breakfast rotation, these three are worth making next.
- High Protein Cottage Cheese Blueberry Muffins
- Ultra Simple Cranberry Protein Muffins Blender Recipe
- Snickerdoodle Protein Muffins The 110 Calorie Gain Hack
Final Thoughts
These are exactly what I want from a fall protein muffin: plenty of apple, a soft center, a real cinnamon crumble, and enough protein that they make sense for breakfast.
Make the full dozen, let them cool, hit them with the cinnamon glaze, and save a few for later. If you make them, leave a comment and let me know what apple you used.
Apple Pie Protein Muffins
Ingredients
- 1 5/8 cups all-purpose flour 195g
- 7/8 cup protein powder 98g
- 1 1/2 cups cup-for-cup zero-calorie sugar alternative
- 2/3 cup plain nonfat Greek yogurt
- 1 cup skim milk
- 1 egg
- 1 1/2 teaspoons vanilla extract
- 1 teaspoon baking soda
- 1/2 teaspoon baking powder
- 1/4 teaspoon salt
- 2 cups peeled diced apples divided: 1 1/2 cups for batter and 1/2 cup for topping
- 1/2 cup cup-for-cup zero-calorie sugar alternative
- 1/3 cup all-purpose flour
- 1/4 cup unsalted butter melted
- 1 teaspoon cinnamon
- powdered sugar amount not measured
- milk as needed
- cinnamon to taste
Method
- Preheat the oven to 350°F and line a 12-cup muffin tin with liners.
- Set aside 1/2 cup of the diced apples for topping the muffins.
- Mix the cinnamon topping ingredients together in a small bowl and set aside.
- In a large bowl, whisk together the sugar alternative, Greek yogurt, egg, and vanilla until combined.
- In a separate bowl, combine the flour, protein powder, baking soda, baking powder, and salt.
- Stir the dry mixture into the yogurt mixture alternately with the skim milk, mixing only until combined.
- Fold in 1 1/2 cups of diced apples.
- Divide the batter evenly among the 12 muffin cups. Add the reserved diced apples and cinnamon topping over the muffins.
- Bake at 350°F for 25-30 minutes, starting to check at 25 minutes. The centers should be set and a toothpick should come out without wet batter.
- Let the muffins cool completely before glazing.
- Mix powdered sugar, milk, and cinnamon until a drizzleable glaze forms. Drizzle over the cooled muffins in a zigzag pattern.
Nutrition
Notes
- Protein powder: Different powders absorb liquid differently. Changing the type or brand can change the batter and finished texture.
- Mixing: Stop once the dry ingredients disappear. Overmixing can make the muffins dense.
- Apples: Dice them small and reserve 1/2 cup for the tops.
- Cooling and glaze: Cool completely before adding the optional cinnamon glaze. Its amounts were not measured; add milk a little at a time until it can be drizzled.
- Nutrition: Estimates are per muffin for a batch of 12 and include the full cinnamon topping. The unmeasured glaze and carbohydrates from the zero-calorie sweetener are excluded; the estimate assumes 0g fat from the protein powder.
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