Apple Protein Muffins
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The best Apple Protein Muffin recipe! Packed with 8g of protein per muffin, these healthy apple muffins are delicious and fluffy!

If you are trying to eat more protein but like a little sweet treat, these Apple Protein Muffins are a must try! Made with only a few simple ingredients, they’re absolutely delicious and SO fluffy!
Plus, each muffin has 8 grams of protein, and they’re easy to make, plus they taste delicious with peanut butter! If you’re looking for other high protein recipes, our Protein Donuts and Protein Blueberry Muffins are 2 of our most popular high protein snacks!
Liz’s Tips for High Protein Apple Muffins
- Dice the apples small. If topping the muffins with extra fruit, only use tiny pieces and avoid placing them in the center of the muffins because they might prevent the tops from doming.
- Use a sweet-tart apple for this recipe, like Granny Smith, Honey Crisp, Braeburn, Fuji, or Pink Lady.
- Use the right protein powder. This was our favorite protein powder in this recipe, but this one also worked well!
Ingredients:

It will also be helpful to have a nonstick muffin tin or silicone muffin liners (we prefer silicone over paper liners).
This was our favorite protein powder in this recipe, but this one also worked well!
substitutions
Greek Yogurt – I used non fat plain Greek yogurt, but I also tested whole milk Greek yogurt. Any fat percentage of plain Greek yogurt will work. I haven’t tried dairy free yogurt in this recipe, so I don’t know how that would work.
Honey – Maple Syrup or even granulated sugar can be used instead of honey in this recipe. Granulated sugar needed a slightly shorter cooking time due to the change in moisture.
Eggs – I did not test any egg replacements in this recipe. If you try one, we would love to know how it worked in the comments below!
Avocado Oil – Any neutral flavored cooking oil can be used in this recipe, including light olive oil or melted coconut oil (that has slightly cooled). If using coconut oil, allow the eggs and Greek yogurt to come to room temperature before starting the recipe to prevent the coconut oil from solidifying.
Oat Flour– Store-bought oat flour or homemade oat flour can be used. I tested a variety of brands in this recipe, and all seemed to produce the same fluffy muffins. If using homemade oat flour, ensure the oats are processed into a very fine flour with no visible oats. Check out our post on how to make homemade oat flour for tips and tricks. If you need this recipe to be gluten-free, be sure to select gluten-free oat flour or gluten-free old-fashioned oats to make oat flour with.
Vanilla Whey Protein Powder – I tested two types of vanilla vegan protein powder in addition to vanilla whey protein and unflavored whey protein (with additional sweetener). This was our favorite protein powder. Review the notes on protein powder below to achieve the best for best results.
Baking Powder & Baking Soda – Both leavening agents are used in these protein muffins because Greek yogurt is acidic. With additional acid in the recipe, it requires an additional base to achieve a good rise.
Apples – Make sure to dice the apple chunks fairly small. Only use very small pieces if you plan to top the muffins with apples. Use a sweet-tart apple for this recipe like Granny Smith, Honey Crisp, Braeburn, Fuji, or Pink Lady. The apple peel can be left on, but peeling will improve the texture a little.
Other Fruit: You can try our Strawberry Protein Muffins, Banana Protein Muffins, or Blueberry Protein Muffin recipe if you want to try this with different fruit.
How to Make Apple Protein Muffins

- Whisk together the oat flour, vanilla protein powder, baking powder, baking soda, cinnamon, salt, ground ginger, and nutmeg.

- In another bowl, whisk together the yogurt, honey, eggs, and oil until smooth.

- Mix the dry ingredients into the wet ingredients thoroughly. Gently fold diced apples into the batter.

- Divide the batter into a prepared muffin tin. Bake at 350° for 16-20 minutes. Allow to cool for about 10 minutes.
Tips for selecting the best protein powder:
I found that whey protein will generally work better for baking compared to vegan alternatives. Whey protein tends to have a simpler ingredient list and act more predictably when adding to a baking recipe. Vegan protein powders can be made from a variety of protein sources, so ingredients can vary quite a bit between brands. This is our favorite protein powder for this recipe.
When selecting a protein powder, look for one that contains whey protein, flavor, sweetener and maybe salt. Additional ingredients beyond that list will add additional variables to the recipe and you can expect slight variations in taste and texture.
Vegan Protein for baking:
We recommend this vegan protein powder in this recipe. The flavor was good and the muffins were a little prettier using this option!
Unsweetened/unflavored protein powder can be used, but you will want to add additional sweetener and vanilla extract to the recipe. I tested using an additional 1/3 cup of honey plus 1 teaspoon of vanilla extract with unflavored whey and that worked, but because of the additional moisture, this batch took longer to bake and was not as pretty but tasted good.

storage
Storing: These muffins can be stored in a gallon-size resealable zipper bag or container at room temperature. Allow muffins to cool fully before storing them in an airtight container to prevent condensation. Enjoy within 4 days for freshness.
Freezing: These high protein apple muffins freeze really well. This is optional but I prefer to flash freeze them for about 20 minutes covered with plastic wrap to prevent them from sticking together. You can do so by freezing the muffins inside the muffin tin after they have cooled at room temperature. Once partially frozen, place the muffins in a resealable freezer bag and store sealed for up to 1 month.
To Thaw: Simply pull the muffins from the freezer and thaw on the counter for about 24 hours, or pop one in the microwave directly from the freezer and microwave for about 30 seconds on high.
Reheating: You can reheat these muffins in the microwave or toaster oven.

other High Protein recipes:
If you want to eat more protein, get our free high protein meals guide. Here are some of our favorite high protein recipes:

Apple Protein Muffin
Ingredients
- ¾ cup fat-free plain Greek yogurt 180 g
- ⅔ cup honey 220 g
- 2 eggs
- ⅓ cup avocado oil
- 2 cups oat flour 210 g
- ½ cup packed vanilla whey protein powder 40 g but will vary based on brand
- 1 teaspoon baking powder
- 1 teaspoon baking soda
- 1 teaspoon ground cinnamon
- ½ teaspoon salt
- ¼ teaspoon ground ginger
- ⅛ teaspoon ground nutmeg
- 1 cup peeled & diced apple peeled (115 g, about 1 medium apple)
Instructions
- Preheat the oven to 350 degrees F. Line a 12-count muffin tin with paper or silicone liners, and set aside.
- Peel the apple and dice it into 1/4-inch square pieces. Set aside.
- In a large mixing bowl, combine the yogurt, honey, eggs, and oil. Whisk together until smooth.
- In a smaller mixing bowl, add the oat flour, vanilla protein powder, baking powder, baking soda, cinnamon, salt, ground ginger, and nutmeg. Whisk together.
- Pour the dry ingredients in a bowl with the wet ingredients and stir together until there are no lumps or streaks of dry ingredients.
- Use a rubber spatula to fold the diced apples into the batter.
- Using a 2-ounce scoop or large spoon, divide the batter between the muffin wells.
- Place the muffins in the oven and bake for 16-20 minutes (17 minutes was perfect for my oven), or until the tops are golden and they can pass the toothpick test.
- Remove the muffins from the oven and allow them to cool for about 10 minutes before enjoying.







Very tasty and super moist muffins!!! I had only 120g honey left and they taste very sweet, I don’t think more is actually needed. Perfect afternoon snack before a workout!!!!
So so tasty!!
Very delicious and a great choice for fall! I was out of nutmeg and ginger so just used pumpkin pie spice as a substitute and still turned out great. These are so good when I need a snack and don’t want to feel guilty. They are packed with protein and so good!
Made the apple ones on the weekend! Yummy & heathy breakfast for my 8 yr old before school! She doesn’t like oats but the oat flour worked great! Used coconut oil and clean simple eats vanilla protein powder
Listen, my daughter requested these again for breakfast this week, so that’s saying something!
Made these this morning and not only did they make the kitchen smell like fall but my preteen and teenager loved them. So happy I made a double match!
Have you ever left skin on the apples? Does it make any difference?
I haven’t tried it, but I wouldn’t recommend it! I think the skin would be tough.