These protein apple muffins are a light, fruity, and oil-free snack and breakfast packed with natural protein to keep you full and energized.
For more easy baking recipes, check out our protein banana bread, apple bread, pumpkin bread, and healthier banana bread.
Light, Fruity Muffins with Natural Protein Power
When you’re craving something sweet yet nourishing, these protein apple muffins are the perfect solution 🍎. Made with wholesome ingredients like Greek yogurt and creamy peanut butter, they’re naturally high in protein and completely oil-free, making them a smart choice for a heart-healthy, fiber-rich snack.
Each bite is soft, lightly sweet, and bursting with apple flavor—just the kind of high protein muffins you’ll want on busy mornings or as an afternoon pick-me-up.
Louise and I love keeping a batch in the freezer so we always have a quick grab-and-go option 🥰. Unlike store-bought muffins, these are made with simple pantry staples, balanced with whole ingredients, and sweetened with fruit (and some sugar).
They’re perfect as protein breakfast muffins or as a post-workout snack that keeps you satisfied without weighing you down. Whether you enjoy them fresh out of the oven or pack them in a lunchbox, these muffins bring both comfort and nourishment 💪.
Ingredients
Find complete ingredient list, quantities, and substitutions in the recipe box at the bottom of the page.
- Apples: fresh, crisp apples bring natural sweetness and moisture. Use pears for a softer flavor, or zucchini for a veggie-packed twist.
- Cinnamon: classic warm spices that highlight the fruit. Try adding pumpkin spice, nutmeg, or apple pie spice for extra coziness.
- Sugar: adds sweetness and helps with texture. Swap with coconut sugar for a more wholesome touch.
- Eggs: bind the muffins and make them fluffy. Vegan? Check out our vegan apple muffins instead.
- Greek yogurt: makes the muffins moist, creamy, and high in protein. Substitute with skyr or dairy-free yogurt for a similar effect.
- Peanut butter: boosts protein and richness. We use one with 100% peanuts, no added sugar or oils. Almond butter, cashew butter, or sunflower seed butter work just as well. This base is what makes them feel like healthy high protein snacks.
- Vanilla extract: enhances sweetness and flavor. Almond extract or maple extract can be fun alternatives.
- All-purpose flour: the best for light, fluffy muffins. Whole wheat flour adds fiber, while oat flour creates a denser, more filling texture.
- Baking powder + baking soda: help the muffins rise. If you’re out, self-rising flour can replace both.
- Optional mix-ins: add chopped nuts, raisins, or even a scoop of protein powder to make these a versatile easy protein muffin recipe.
How to Make Protein Apple Muffins
Step 1 – Prep the Apples
Preheat your oven to 350°F (180°C) and line a 12-cup muffin pan with liners. Dice 1 apple (no need to peel) into small cubes, then toss with cinnamon and 1 tablespoon of sugar. Set aside—this quick marinade will add juicy bursts of sweetness inside your muffins.
Step 2 – Mix the Wet Ingredients
In a large mixing bowl, whisk together the eggs, Greek yogurt, peanut butter, sugar, and vanilla extract until smooth. Grate in 2 more apples and stir to combine. This blend makes the muffins naturally moist and protein-rich, just like the best greek yogurt muffins.
Step 3 – Add the Dry Ingredients
Sprinkle the flour, baking powder, and baking soda over the wet mixture. Gently fold everything together until just combined. Avoid overmixing—this keeps your healthy apple muffins light and fluffy.
Step 4 – Fold in the Apples
Take the cinnamon-sugar apple cubes you set aside and fold them into the batter. Each bite will have soft, spiced apple pieces.
Step 5 – Bake the Muffins
Spoon the batter evenly into the prepared muffin pan. For a bakery-style finish, sprinkle a little extra cinnamon sugar on top. Bake for 22–25 minutes, or until a toothpick inserted in the center comes out mostly clean.
Let the muffins rest in the pan for 5 minutes before moving them to a wire rack. They’re delicious warm, but also perfect to freeze for meal prep.
Tips
- Choose the right apples: tart apples like Granny Smith balance the sweetness, while Honeycrisp makes the muffins extra juicy.
- Don’t skip the marinated apples: tossing diced apple in cinnamon sugar adds pockets of flavor and keeps them moist.
- Use room-temperature eggs and yogurt: this helps the batter mix smoothly and gives you fluffier results, this is true for any easy protein muffin recipe.
- Don’t overmix the batter: stir until just combined—overmixing can make muffins tough instead of light.
- Add extra protein if you want: stir in a scoop of vanilla protein powder for more protein breakfast muffins without changing the texture much.
- Customize your mix-ins: walnuts, raisins, or dark chocolate chips all work beautifully in these peanut butter muffins.
- Check early for doneness: ovens vary, so start testing at 20 minutes with a toothpick in the center.
- Cool before storing: let muffins cool fully on a rack before freezing or storing in a container to keep them fresh longer.
Frequently Asked Questions
Yes! Just swap the flour with a 1:1 gluten-free blend for delicious gluten free muffins.
Nope—leaving the peel on adds color, fiber, and texture, but you can peel if you prefer.
Not in this case. Since these muffins are already very moist from apples, Greek yogurt, and peanut butter, adding liquid sweeteners would make the texture too dense and wet. Instead, you can use coconut sugar, light brown sugar, or date sugar for a more natural option while keeping the structure light and fluffy.
Keep them in an airtight container at room temp for 2 days or freeze for longer freshness.
Yes, almond or cashew butter both work well.
Definitely—they freeze beautifully and make a great option for healthy high protein snacks. Also, they stay moist for days!
More Easy Baking Recipes
- Vegan Carrot Cake
- Easy Apple Cake
- Chocolate Banana Bread
- Apple crumble
- Pear Cake
- Easy Vanilla Cake (No Layers)
- Banana zucchini bread
- Blueberry muffins
- Orange Cake
If you tried this Protein Apple Muffins recipe or any other recipe on our blog, please leave a 🌟 star rating and let us know how it goes in the comments. We love hearing from you!
Protein Apple Muffins
Equipment
- 12-cup muffin pan
Ingredients
- 3 apples divided — 2 grated, 1 cut into small dice
- 1 teaspoon cinnamon + ¼ tsp nutmeg optional
- ½ cup sugar + 1 tablespoon for marinading the apples — you can go down to ¼ cup for less sweet
- 2 large eggs
- ⅔ cup Greek yogurt
- ⅓ cup peanut butter — we use one with 100% peanuts, no added sugar or oils.
- 1 tablespoon vanilla extract
- 1½ cups all-purpose flour
- 2 teaspoons baking powder
- 1 teaspoon baking soda
Instructions
- Prep the Apples: Preheat the oven to 350°F (180°C). Line you muffin pan with muffin liners.Dice 1 apple (peel on) into small cubes. Toss with 1 teaspoon cinnamon and 1 tablespoon sugar. Set aside.
- Mix the Wet Ingredients: In a large bowl, whisk together 2 large eggs, ⅔ cup Greek yogurt, ⅓ cup peanut butter, ½ cup sugar, 1 tablespoon vanilla extract.Grate in 2 apples (cored and seeded) and toss until combined.
- Add the Dry Ingredients: Add 1½ cups all-purpose flour, 2 teaspoons baking powder, and 1 teaspoon baking soda.Gently fold until just combined. Don’t overmix.
- Fold in Diced Apples: Add the diced, marinated apples to the batter and stir lightly.
- Bake the Muffins: Divide the batter evenly into a lined 12-cup muffin pan. Sprinkle tops with a little cinnamon sugar (optional).Bake at 350°F (180°C) for 22–25 minutes, until a toothpick comes out mostly clean.Let muffins cool in the pan for 5 minutes, then transfer to a wire rack.
Notes
- Apples → swap with pears for gentle sweetness or zucchini for a veggie twist.
- Cinnamon → try pumpkin spice, nutmeg, or apple pie spice for extra coziness.
- Sugar → use coconut sugar or date sugar for a more wholesome touch.
- Eggs → need vegan? Check out our vegan apple muffins recipe.
- Greek yogurt → replace with skyr or dairy-free yogurt for the same creamy, protein boost.
- Peanut butter → almond, cashew, or sunflower butter make these healthy high protein snacks too.
- Vanilla extract → almond or maple extract both add fun flavor.
- All-purpose flour → whole wheat for extra fiber or oat flour for a denser bite.
- Baking powder + soda → out of both? Use self-rising flour instead.
- Optional mix-ins → chopped nuts, raisins, or protein powder turn these into an easy protein muffin recipe.
- Pick the right apples → Granny Smith for tartness, Honeycrisp for juicy sweetness.
- Marinate the apples → cinnamon sugar keeps them moist and adds flavor bursts.
- Room-temperature eggs & yogurt → makes batter smoother and fluffier.
- Don’t overmix → stir until just combined for light, tender muffins.
- Boost the protein → add a scoop of vanilla powder for extra protein.
- Mix it up → try walnuts, raisins, or dark chocolate.
- Test early → check doneness at 20 minutes since ovens vary.
- Cool completely → let muffins rest before storing or freezing to lock in freshness.
Nutrition
Hi! We are Nico & Louise
We’re here to share delicious, easy, and healthy plant-based recipes (vegetarian & vegan) 🌿✨.
Welcome to our blog, we are glad you are here.
Very delicious 😋, easy to do
Lovely and moist. Full of flavour
This recipe looks like a fabulous option to try. Am looking forward to making it.
Made these today for 1st Day of School in NYC!
I already ate 2! They are divine! Thank you!