These Healthy Apple Cinnamon Muffins are moist, fluffy and made with whole wheat pastry flour, Greek yogurt, pure maple syrup and fresh apple. Packed with warm cinnamon and cozy fall flavor, these wholesome muffins make the perfect easy breakfast or snack!
Please enable JavaScript in your browser to complete this form.
It’s officially apple season, which means it’s time for all the cozy fall baking! These Healthy Apple Cinnamon Muffins are soft, fluffy and packed with fresh shredded apple and warm cinnamon in every bite. They’re naturally sweetened with pure maple syrup and made with Greek yogurt and whole wheat pastry flour for a wholesome twist on classic apple muffins.
Best of all, these muffins come together in just 30 minutes and are perfect for the whole family. Enjoy them warm for breakfast, pack them in lunchboxes or keep a batch on hand for an easy afternoon snack. You can even freeze them for later!
Why You’ll Love These
Moist and fluffy – Greek yogurt and shredded apple keep these muffins soft and tender without needing a lot of oil.
Naturally sweetened – pure maple syrup adds just the right amount of sweetness without refined sugar.
Made with wholesome ingredients – whole wheat pastry flour adds whole grains while still keeping the texture light.
Perfect for fall – fresh apples and warm cinnamon make these such a cozy breakfast or snack.
Easy to make – the batter comes together quickly and the muffins are ready in about 30 minutes.
Great for meal prep – make a batch for easy breakfasts, lunchboxes and snacks throughout the week.
Ingredients You’ll Need
whole wheat pastry flour – my favorite flour for healthier baking because you get the benefits of whole grains while still keeping the muffins light and tender. You can also use white whole wheat flour, all-purpose flour or a 1-to-1 gluten-free baking flour.
baking soda – helps the muffins rise and gives them a soft, fluffy texture.
cinnamon – adds that warm, cozy spice that pairs perfectly with fresh apples.
salt – enhances all the flavors and balances the sweetness.
apple – you’ll need about one medium apple, peeled and shredded. I love Honeycrisp, but Granny Smith, Pink Lady, Braeburn and Golden Delicious are all great choices.
eggs – give the muffins structure and help them rise.
pure maple syrup – naturally sweetens the muffins without refined sugar. Honey can also be used.
Greek yogurt – adds moisture and tenderness while allowing us to use less oil. I recommend plain Greek yogurt.
milk – I use unsweetened almond milk, but any milk you have on hand will work.
coconut oil – just 3 tablespoons adds moisture and helps create a soft, tender crumb. Melt it and let it cool slightly before adding it to the batter.
vanilla extract – adds a little extra warmth and sweetness to the muffins.
Best Apples for Apple Cinnamon Muffins
I love using Honeycrisp apples because they’re naturally sweet with a little tartness and hold up really well when baked. Granny Smith is another great choice if you prefer a more tart apple flavor.
Other good baking apples include Pink Lady, Braeburn and Golden Delicious. You can even use a combination of sweet and tart apples if you’re making a double batch.
For this recipe, I prefer to shred the apple rather than dice it. Shredded apple distributes evenly throughout the batter and adds moisture and apple flavor to every bite without leaving large chunks. You can leave the peel on if you prefer, but I usually peel the apple first for the softest muffin texture.
How to Make Healthy Apple Cinnamon Muffins
Prep the apple. Preheat the oven to 350°F and spray a 12-cup muffin pan with nonstick cooking spray or line with paper liners. Peel the apple and shred it using the large holes of a box grater.
Mix the dry ingredients. In a large bowl, whisk together the whole wheat pastry flour, baking soda, cinnamon and salt.
Combine the wet ingredients. In a separate bowl, whisk together the eggs, maple syrup, Greek yogurt, milk, melted and cooled coconut oil and vanilla until smooth and well combined.
Make the batter. Pour the wet ingredients into the dry ingredients and gently mix with a spatula just until combined. Be careful not to overmix.
Fold in the apple. Gently fold the shredded apple into the batter until evenly distributed.
Fill the muffin cups. Divide the batter evenly between 12 muffin cups, filling each almost to the top.
Bake. Bake for 18 to 22 minutes, or until the tops are set and a toothpick inserted into the center comes out clean. Mine are usually perfect around 20 minutes.
Cool and enjoy. Let the muffins cool in the pan for about 5 minutes before transferring them to a wire rack to finish cooling.
Tips for Moist and Fluffy Apple Muffins
Don’t overmix the batter. Mix only until the flour is incorporated. Overmixing can make muffins dense or tough.
Use whole wheat pastry flour. Regular whole wheat flour is heavier and can produce a denser muffin, while whole wheat pastry flour gives you a much softer texture.
Measure your flour correctly. Spoon the flour into your measuring cup and level it off rather than scooping directly from the bag, which can pack in too much flour.
Use finely shredded apple. Shredding distributes the moisture throughout the batter and gives you apple in every bite.
Don’t squeeze out the apple. We want that natural apple moisture in the muffins!
Use room-temperature ingredients when possible. This helps everything combine more evenly, especially when working with melted coconut oil.
Don’t overbake. Start checking around 18 minutes. The muffins are done when a toothpick inserted in the center comes out clean or with just a few moist crumbs.
Let them cool briefly in the pan. Five minutes is plenty before moving them to a wire rack so the bottoms don’t become soggy.
What to Serve with Apple Cinnamon Muffins
These muffins are delicious on their own for breakfast or a snack, but you can easily turn them into a more filling breakfast.
Greek yogurt – pair a muffin with Greek yogurt and fresh fruit for an easy protein-packed breakfast.
Eggs – serve alongside scrambled eggs, hard-boiled eggs or an egg casserole for extra protein.
Smoothie – a fruit or protein smoothie makes these muffins an easy grab-and-go breakfast.
Fresh fruit – serve with berries, banana slices or extra fresh apple.
Nut butter – spread a warm muffin with peanut butter or almond butter for a satisfying snack.
Oatmeal – pair with a smaller serving of oatmeal or these apple pie overnight oats for an extra-cozy fall breakfast.
Frequently Asked Questions
No, you don’t have to peel the apple, but I prefer to for the softest texture. If you don’t mind little pieces of peel throughout your muffins, feel free to leave it on.
Yes! You can substitute all-purpose flour using the same amount. The muffins may be slightly lighter in texture. White whole wheat flour or a 1-to-1 gluten-free baking flour can also work.
Yes. Unsweetened applesauce, mashed banana or pumpkin puree can be substituted for the Greek yogurt, although each will change the flavor and texture slightly.
A 1-to-1 gluten-free baking flour should work in place of the whole wheat pastry flour.
Absolutely! These muffins freeze really well. Let them cool completely before placing them in a freezer-safe container or ziplock bag and freeze for up to 3 months. Thaw at room temperature or warm briefly in the microwave before serving.
Pin this now to find it later
Follow on Instagram
More Apple Recipes You’ll Love
Apple Cinnamon Thumbprint Cookies
More Muffin Recipes You’ll Love
Chocolate Chip Banana Zucchini Muffins
Lemon Blueberry Blender Muffins
Strawberry Jam Filled Oat Muffins
Hope you all enjoy these Healthy Apple Cinnamon Muffins and if you love this as much as we do, please leave me below and don’t forget to tag me on Instagram using the hashtag #eatyourselfskinny! I love seeing all your delicious recreations!
Healthy Apple Cinnamon Muffins
Ingredients
Instructions
Notes
Freezing: Let the muffins cool completely, then place in a freezer-safe bag or container and freeze for up to 3 months. Thaw at room temperature or microwave for about 30 to 40 seconds until warmed through.
Make ahead: These muffins are perfect for meal prep and can be baked ahead for easy breakfasts and snacks throughout the week.
Nutrition