apple protein muffins with one split in half on a plate — Makes: *12 Servings*
Per Serving: *12g Protein | 175 Cal*

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Fall flavors are on my mind from that first hint of seasons changing. Apple, cinnamon, nutmeg, maple, pumpkin, they’re all just so cozy and comforting! But a lot of fall treats are high in calories and low in nutrients like protein, which you know I take seriously around here. That’s why I created these high-protein apple muffins, packed with warm baking spices, sweet apples, and plenty of protein. They're a delicious way to indulge in the flavors of the season without having to sacrifice or compromise on your overall health and wellness goals.

These fluffy muffins embrace the season with flavors like cinnamon, nutmeg, and allspice, while also loaded up on protein thanks to cottage cheese, eggs, and a blend of protein powders that give them serious staying power. With a crunchy-sweet crumble topping and plenty of fresh apple chunks, enjoy these muffins for breakfast, meal prep, or the perfect snack any time of the day.

Ready in about 30 minutes and full of wholesome ingredients, this is one easy recipe you’ll want to make on repeat this fall!

Why You’ll Love These Apple Pie Protein Muffins

High in protein: These muffins are a great choice if you’re trying to boost your protein intake. Each muffin has about 10-12 grams of protein, depending on whether or not you choose to add the crumble topping.
Bursting with your favorite fall flavors: With warm baking spices and fresh chunks of apple, these muffins are basically a healthier apple pie, just in muffin form.
Great for meal prepping: Muffin recipes are always a good choice when it comes to meal prep because you can make a batch on Sunday and then have healthy, protein-packed breakfasts or snacks all week long.
Easy to customize and make your own: It’s so easy to make this protein muffins recipe your own. Use your favorite sweetener, try a different flavor or protein powder, switch up the spices, or even the fruit!

apple protein muffins in the background, with a close-up shot of one muffin on a plate in the foreground

Ingredients

Wet Ingredients

¾ cup low-fat cottage cheese, blended until smooth
2 large eggs
¼ cup maple syrup or honey
¼ cup applesauce

Dry Ingredients

60g vanilla whey protein powder (about 2 scoops)
30g casein protein powder (about 1 scoop)
1 ¼ cups oat flour
1 ½ teaspoons baking powder
2–4 tablespoons coconut sugar (adjust to sweetness)
¼ teaspoon baking soda
¼ teaspoon salt
2 teaspoons cinnamon
½ teaspoon nutmeg
½ teaspoon allspice

Mix-In

½ apple, finely diced (Honeycrisp or another firm variety)

Topping

½ apple, finely diced

Crumble Topping (optional)

1 scoop vanilla whey protein powder
2 tablespoons oat flour
4 tablespoons coconut sugar
1 tablespoon butter, melted
Pinch of salt

Instructions

Preheat the oven: Turn on the oven and set it to preheat to 400 degrees F. Line a muffin tin with 12 muffin liners or squares of parchment paper. If needed, grease the muffin tin well with a neutral oil instead.
Mix the wet ingredients: Place the blended cottage cheese, eggs, maple syrup, and applesauce in a large bowl. Whisk well to combine.
Mix the dry ingredients: To a separate bowl, add the vanilla protein powder, casein protein powder, oat flour, baking powder, coconut sugar, baking soda, salt, and spices. Whisk to combine.
Mix the batter: Add the dry ingredients to the bowl of wet ingredients and use a rubber spatula to fold the dry ingredients into the wet ingredients until just combined. Do not overmix.
Add the apple: Stir in half the diced apple.
Fill the muffin tin: Fill each muffin liner with a bit of batter, making sure each muffin is even. Sprinkle the other half of the diced apple over the tops of the muffins.
Make the crumble topping: In a small bowl, mix together the whey protein powder, oat flour, sugar, butter, and salt until it has the texture of wet sand. Sprinkle it over each muffin to add a sweet and crunchy touch.
Bake the muffins: Transfer the muffin tin to the preheated oven and bake at 400 degrees F for 5 minutes, then lower the oven temperature to 350 degrees F and bake the muffins for 20 more minutes, or until they're golden brown and a tester inserted into the center comes out clean.
Cool: Transfer to a wire rack and cool. Enjoy!

Nutrition Info (Per Muffin - Makes 12 Muffins)

Without topping

Calories: 140
Protein: 10g
Carbs: 20g
Fat: 3g

With topping

Calories: 175
Protein: 12g
Carbs: 23g
Fat: 4g

overhead shot of protein muffins with one apple muffin on a plate

Swaps & Substitutions

Protein powder: When I’m baking with protein powder, I prefer a blend of whey and casein protein powders for the best results, texture-wise (you'll get a more tender crumb), but if needed, you can use only whey protein powder or even a plant-based protein powder instead. Just know that the texture may not be quite as good as if you’d used the blend.
Sweeteners: If you don’t want to use coconut sugar, no problem at all! You can swap it out in favor of brown sugar, monk fruit, or stevia. Just make sure you adjust the amount if needed. You don’t want to add way too much accidentally.
Cottage cheese: If you don’t have any cottage cheese on hand, you can use plain Greek yogurt (or a plant-based yogurt) instead, but the texture of the muffins may not be exactly the same.
Fruit: I love using Honeycrisp apples in these muffins, but if you’re looking for a different option, try Granny Smith for a bit more tartness. You could also use late-season peaches or early pears, if you’d like.

Pro Tips for the Best Healthy Protein Muffins

Make sure you blend the cottage cheese until fully smooth. It’ll make the batter extra rich instead of super lumpy and it only takes a minute or two.
Don’t just bake the muffins for 25 minutes at 350—that first 5-minute blast of 400 degree air helps your muffin top rise.
Store leftover muffins in an airtight container in the fridge for up to 5 days or freeze individually in freezer bags or freezer-safe containers (or wrap tightly with plastic wrap).

FAQs

If you want to make gluten-free muffins, make sure you’re using a certified gluten-free oat flour. Most oat flours will be naturally gluten-free, but if you need them to be strictly gluten-free because of an allergy or illness, you’ll want to use flour that’s certified.
Nope! Your muffins will be just a delish without the crumble topping, but it does add a little extra sweetness and hint of crunch. Plus, it adds a bit more protein to your muffin and makes it feel more like a bakery treat. What’s not to like, right?
No! The apples and spices temper any protein powder flavor and the cottage cheese and applesauce keep the muffins plenty moist.
These apple protein muffins are delicious served at room temperature or warmed up. If you’d like to serve them warm, you can gently warm them in a 300-degree F oven for about 5 minutes or microwave them for about 15-20 seconds.

These apple protein muffins are the perfect quick snack as the weather gets cooler: cozy, warmly spiced with a hint of sweetness, and with enough protein to fill you up. Ideal for fall meal prepping or an on-the-go treat, they’re a macro-friendly way to enjoy all of the flavors of the season.

Apple Protein Muffins

Yield: 12

Author: Ashley aka The Protein Snack Queen

These healthy apple protein muffins are the perfect fall meal-prep treat. With a decadent crumb topping and 10-12g of protein per muffin, these are a macro-friendly way to indulge in the flavors of the season.