Healthy Apple Cinnamon Muffins – Eat Yourself Skinny

These Healthy Apple Cinnamon Muffins are soft, fluffy and packed with fresh shredded apple, warm cinnamon and cozy fall spices. Made with Greek yogurt, whole wheat pastry flour and pure maple syrup, then topped with cinnamon sugar for the perfect bakery-style muffin!

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

• Soft and fluffy – a combination of all-purpose and whole wheat pastry flour gives these muffins a light, tender texture.
• Naturally sweetened – the muffin batter is sweetened with pure maple syrup, with just a touch of cane sugar on top for that bakery-style finish.
• 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.
• all-purpose flour – using some all-purpose flour keeps these muffins soft, light and fluffy.
• baking powder + baking soda – using both gives these muffins plenty of lift and helps create those tall, fluffy muffin tops.
• cinnamon + nutmeg – warm spices that pair perfectly with fresh apple and give these muffins their cozy fall flavor.
• 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 muffin batter and adds moisture. 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.
• olive oil – adds moisture and keeps the muffins soft without using butter. Use a mild-flavored olive oil so it doesn’t overpower the apple and cinnamon.
• vanilla extract – adds a little extra warmth and sweetness to the muffins.
• cinnamon sugar topping – a simple mixture of cane sugar and cinnamon sprinkled over the muffins before baking gives them a sweet, bakery-style finish.

How to Make Healthy Apple Cinnamon Muffins

1. Prep the apple. Preheat the oven to 425°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.
2. Mix the dry ingredients. In a large bowl, whisk together the whole wheat pastry flour, all-purpose flour, baking powder, baking soda, cinnamon, nutmeg and salt.
3. Combine the wet ingredients. In a separate bowl, whisk together the eggs, maple syrup, Greek yogurt, milk, olive oil and vanilla until smooth and well combined.
4. 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.
5. Fold in the apple. Gently fold the shredded apple into the batter until evenly distributed.
6. Rest the batter. Let the batter sit at room temperature for 10 to 15 minutes. This allows the flour to hydrate and the batter to thicken, helping create taller, fluffier muffin tops. Don’t stir the batter again after resting.
7. Make the cinnamon sugar topping. While the batter rests, combine the cane sugar and cinnamon in a small bowl.
8. Fill the muffin cups. Divide the batter evenly between 12 muffin cups, filling each almost to the top. Sprinkle the cinnamon sugar mixture evenly over each muffin.
9. Bake. Bake at 425°F for 5 minutes, then, without opening the oven door, reduce the temperature to 350°F. Continue baking for another 13 to 16 minutes, or until the muffin tops are domed and a toothpick inserted into the center comes out clean.
10. 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

• Use room-temperature ingredients. This is especially helpful with the eggs and Greek yogurt so the batter combines evenly.
• Don’t overmix. Gently fold the batter just until combined for the softest, fluffiest texture.
• Lightly blot the apple. Shredded apples can release quite a bit of liquid. Remove some excess moisture without squeezing them completely dry.
• Let the batter rest. That 10 to 15-minute rest gives the flour time to hydrate and helps the batter thicken before baking.
• Don’t stir after resting. Scoop the rested batter directly into the muffin cups so you don’t knock out the air that’s developed.
• Fill the cups almost to the top. This helps create those big bakery-style muffin tops.
• Start with high heat. The initial 425°F blast gives the muffins a quick rise. Lowering the oven to 350°F allows the centers to finish baking without over-browning the tops.
• Don’t open the oven when lowering the temperature. Simply change the setting from 425°F to 350°F and keep the door closed.
• Don’t overbake. Start checking after the additional 13 minutes at 350°F.

Variations and Substitutions

• Add nuts – chopped walnuts or pecans would be delicious.
• Add raisins – fold in raisins or dried cranberries for extra sweetness and texture.
• Add more spice – add a little ginger, cloves or apple pie spice for even more fall flavor.
• Skip the topping – you can leave off the cinnamon sugar if you’d prefer the muffins without added cane sugar.
• Use a different oil – melted coconut oil or avocado oil can be substituted for the olive oil.
• Make mini muffins – for mini muffins, I wouldn’t use the high-temperature method because they bake so quickly. Bake them entirely at 350°F and start checking around 10 minutes.

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

More Apple Recipes You’ll Love

More Muffin Recipes You’ll Love

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!