Healthy Apple Muffins
Published on October 24, 2025
Quick Summary
These Healthy Apple Muffins are soft, perfectly spiced, and naturally sweetened with applesauce and maple syrup. Made with Greek yogurt for extra moisture and protein, they’re a wholesome breakfast or snack everyone will love. Enjoy them warm from the oven for the coziest fall treat!
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Pin ItYou’ll Fall in Love with These Healthy Apple Muffins
When apple season rolls around, I can’t resist baking something warm and cozy and these Healthy Apple Muffins are one of my favorites. They’re everything you want in a fall muffin: soft, tender, and filled with warm spices. Thanks to applesauce and freshly grated apple, every bite is bursting with real apple flavor.
I love that they taste indulgent but are actually made with better-for-you ingredients. The Greek yogurt keeps them moist and pure maple syrup adds the perfect natural sweetness. Plus, your kitchen will smell amazing while they bake; like a fall candle, but better.
These muffins are perfect for busy mornings, lunch boxes, or an afternoon snack with a cup of coffee or tea. I often bake a batch on Sunday and enjoy them throughout the week. They freeze beautifully, too, so you can always have a healthy treat ready to go.
If you’re looking for a cozy, feel-good muffin recipe that’s still wholesome, this is it. You’ll make them once and want to bake them all season long!
Ingredients You’ll Need (& Helpful Notes)
- Flour: You can use all-purpose or white whole wheat flour for a slightly heartier texture.
- Spices: Cinnamon, nutmeg, and cloves give the muffins that classic fall flavor. Don’t skip them!
- Greek Yogurt: Adds protein and keeps the muffins soft and moist. Use plain, not flavored.
- Applesauce: Naturally sweetens and replaces some of the oil. Make sure it’s unsweetened.
- Maple Syrup: Pure maple syrup adds a lovely depth of sweetness—no refined sugar needed.
- Avocado Oil: A heart-healthy oil that keeps the texture tender. You can also use melted coconut oil or vegetable oil.
- Eggs: Bring them to room temperature for the best rise.
- Vanilla Extract: Enhances all the warm, cozy flavors.
- Apple: I love using a Honeycrisp for its sweetness and texture, but any crisp apple works. Grate it fresh!
- Turbinado Sugar: Sprinkled on top for a bakery-style sparkle and slight crunch.
Tips for Making the Best Healthy Apple Muffins
- Bring ingredients to room temperature. Let the eggs and yogurt sit out for about 20–30 minutes before you start.
- Don’t overmix. Stir the wet and dry ingredients together until just combined for tender muffins.
- Use paper liners AND spray them. This helps prevent sticking, especially with healthier batters.
- Fill the muffin cups to the top. You’ll get beautifully tall, bakery-style muffins.
- Add a sprinkle of turbinado sugar. It gives the tops a gorgeous golden sparkle and just the right amount of crunch.
- Test for doneness. A toothpick should come out clean or with just a few moist crumbs.
- Let them cool. They set up as they rest, resist eating them straight from the oven (even though it’s hard!).
Healthy Apple Muffins
Ingredients
- 2 cups all-purpose flour (or white whole wheat flour)
- 1 1/2 teaspoons baking powder
- 1 1/2 teaspoons ground cinnamon
- 1/2 teaspoon baking soda
- 1/2 teaspoon salt
- 1/4 teaspoon ground nutmeg
- 1/4 teaspoon ground cloves
- 1/2 cup plain Greek yogurt, at room temperature
- 1/2 cup applesauce
- 1/2 cup pure maple syrup
- 1/3 cup avocado oil
- 2 large eggs, at room temperature
- 1 1/2 teaspoons vanilla extract
- 1 cup grated Honeycrisp apple, 1 large apple
- Turbinado sugar, for sprinkling on top
Instructions
- Preheat oven to 375 degrees F. Line a muffin tin with paper liners and spray them with nonstick cooking spray. Set aside.
- In a large bowl, whisk together the flour, baking powder, cinnamon, baking soda, salt, nutmeg, and cloves. Set aside.
- In a medium bowl, whisk together the applesauce, Greek yogurt, maple syrup, oil, eggs, and vanilla extract.
- Add the wet ingredients to the dry ingredients and stir until just combined. Don’t over mix. Gently fold in the grated apple.
- Divide the batter equally amongst the muffin cups, filling them to the top. Sprinkle the tops generously with turbinado sugar.
- Bake for 18 to 24 minutes or until the muffins are golden brown and the tops of the muffins bounce back when you gently press on them. You can also insert a toothpick into the center of a muffin, if it comes out clean, they are done.
- Let the muffins cool in the pan for 5 minutes. Remove muffins from the tin let cool another 15 minutes. Enjoy!
Notes
- Room Temperature: Store cooled muffins in an airtight container for up to 3 days on the counter.
- Freeze: Freeze muffins in a freezer-safe bag or container for up to 3 months. Thaw at room temp or reheat in the microwave for a warm, fresh taste.
Nutrition
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