Healthy Apple Muffins
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These healthy apple muffins are naturally sweetened with maple syrup and packed with fall flavors. They’re so delicious that your family and friends won’t know this cinnamon apple muffin recipe is also nourishing and wholesome!
Recipe Overview
- Flavor: Warm, mildly sweet, and spiced with cinnamon, nutmeg, and cloves.
- Texture: Soft, tender, and moist, thanks to the addition of shredded apple and applesauce.
- Time: Just over 30 minutes (32 minutes total, depending on how quickly you shred the apple).
- Yield: Twelve servings
Why I Love These Healthy Muffins
There's nothing more comforting than the scent of apples and warm spices filling the kitchen on a crisp fall morning. These Healthy Apple Muffins are mildly sweet, perfectly moist, and naturally flavored with cinnamon, nutmeg, and cloves. They're a wholesome breakfast, cozy afternoon pick-me-up, or a delightful teatime treat.
Inspired by my very popular Healthy Pumpkin Muffins, this apple version is made with better-for-you ingredients like applesauce, shredded apple, and maple syrup. They're quick and easy to make - about 30 minutes from start to finish - and always a hit with family and friends.
Jump to:
Ingredients
Here's what you'll need to make these cozy apple muffins:
- Cooking oil - Use vegetable oil, olive oil, or melted coconut oil. Each brings a slightly different flavor profile.
- Maple syrup - A natural sweetener that adds gentle caramel notes.
- Large eggs - For structure and richness.
- Unsweetened applesauce - Adds natural sweetness and keeps the muffins moist.
- Spices & Seasonings - Cinnamon, nutmeg, cloves, and a pinch of salt bring warmth and balance.
- Baking powder & baking soda - Give the muffins their rise.
- Shredded apple - Fresh apple adds texture, sweetness, and juiciness. Leave the peel on for extra nutrients.
- Flour - Use all-purpose flour for the highest rise, whole wheat for more nutrients, or a blend of both.
- Optional topping: Turbinado (raw) sugar for a delightful bakery-style crunch.
How to Make Apple Muffins
Preheat the oven to 425°F and grease a 12-cup standard-size muffin tin with nonstick cooking spray, or line with paper cups.
- Step 1: In a large bowl, whisk together the flour, baking powder, baking soda, salt, cinnamon, nutmeg, and cloves.
- Step 2: In a medium bowl, whisk together oil, applesauce, maple syrup, and eggs until combined. Pour the oil mixture into the flour mixture and mix until combined.
- Step 3: Shred the apple on a box grater (peeled or unpeeled). Then fold into the muffin batter.
- Step 4: Divide the batter evenly among the muffin cups and sprinkle raw sugar over the top if desired. Bake for 5 minutes at 425℉. Reduce the oven temperature to 350°F. Bake for an additional 15-16 minutes.
Cooling: Remove the muffin tin from the oven and set it on a rack to cool for 10 minutes. Enjoy!
Variations
- Add nuts - Fold in ½ cup chopped walnuts or pecans for crunch.
- Boost protein - Mix in 2 tablespoons of ground flaxseed or chia seeds.
- Mini Muffins - Make bite-sized muffins by scooping the batter into a mini muffin tin. Bake 12-14 minutes, or until a toothpick comes out clean.
- Apple Loaf - Turn this recipe into a cozy quick bread by baking the batter in a greased 8×4-inch loaf pan. Bake at 350°F for 45-55 minutes, tenting with foil if the top browns too quickly.
Serving Ideas
- Warm with a smear of butter, or my favorite option: apple butter. I love this easy, naturally sweetened apple butter recipe.
- As a grab-and-go breakfast with Greek yogurt.
- On an afternoon tea tray with scones (these fall scone recipes are delicious) and fruit.
- Pair with a cozy fall drink, such as chai tea, cinnamon tea, or hot cider.
Storage
- Freezer: Freeze cooled muffins in a freezer bag up to 3 months. Thaw overnight in the fridge or warm briefly in the microwave.
- Room temperature: Store in an airtight container for up to 3 days.
- Refrigerator: Keep up to 5 days.
Baking Tip: How to Measure Flour
Getting your flour measurement right is one of the simplest ways to guarantee tender, moist muffins instead of dry or dense ones. It might surprise you, but scooping flour directly with a measuring cup can pack in up to 50% more than the recipe calls for. That extra flour makes a big difference in texture.
For the most accurate results, use the spoon and level method:
- Fluff - Stir the flour lightly in its container or bag to loosen it.
- Spoon - Use a large spoon to scoop flour into your measuring cup. Avoid dipping the cup straight into the flour, which compacts it.
- Level - Run the flat edge of a knife across the top of the cup to level it off.
👉 This simple step ensures your muffins bake up light, moist, and flavorful every time.
Recipe FAQs
I recommend a sweet-tart variety like Honeycrisp, Fuji, or Gala. These shred easily, hold moisture, and balance beautifully with warm spices. Very tart apples (like Granny Smith) may make the muffins less sweet.
I like to use white whole wheat flour - it's lighter than traditional whole wheat but still adds nutrients and fiber. All-purpose flour will give you the highest rise and the most tender crumb, while 100% whole wheat will make the muffins heartier and denser. A mix of the two also works well.
"Healthy" can mean different things, but these muffins are made with better-for-you swaps: maple syrup instead of refined sugar, applesauce for moisture, and fresh apples. They're naturally sweetened and higher in fiber than many traditional muffin recipes.
Yes - use a 1:1 gluten-free flour blend that includes xanthan gum for structure. The texture will be slightly different, but still moist and flavorful.
Store in an airtight container at room temperature for 2-3 days, refrigerate up to 5 days, or freeze for up to 3 months. Thaw overnight or warm gently in the microwave before serving.
Definitely! Chopped walnuts or pecans add crunch, and dried fruit like raisins or cranberries brings extra sweetness. For a treat, fold in a handful of dark chocolate chips.
More Easy Muffin Recipes to Try
Looking for other muffin recipes like this? Try these:
- Panera Pumpkin Muffins
- Streusel Blueberry Muffin Bread
- Easy Carrot Cake Muffins
- Easy Carrot Muffins (Naturally Sweetened)
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Healthy Apple Spice Muffins Recipe
Equipment
Ingredients
- 1 ¾ cup flour like white whole wheat, whole wheat or a mix of your favorite flour.
- 1 teaspoon baking powder
- 1/2 teaspoon baking soda
- 3/4 teaspoon salt
- 2 teaspoons ground cinnamon
- 1/2 teaspoon nutmeg
- 1/4 teaspoon ground cloves
- 1/2 cup cooking oil olive oil, melted coconut oil, etc
- 1/2 cup unsweetened applesauce
- 1/3 cup maple syrup
- 2 large eggs
- 1 teaspoon vanilla extract
- 1 cup shredded apple
- OPTIONAL: Turbinado raw sugar for topping
Instructions
- Preheat the oven to 425°F and grease a 12-cup standard-size muffin tin with nonstick cooking spray, or line with paper cups.
- In a large bowl, whisk together the flour, baking powder, baking soda, salt, cinnamon, nutmeg, and cloves.
- In a medium bowl, whisk together oil, applesauce, maple syrup, and eggs until combined. Pour the oil mixture into the flour mixture and mim until combined. Fold in the shredded apples.
- Divide the batter evenly among the muffin cups and sprinkle raw sugar over the top if desired.
- Bake for 5 minutes at 425℉. Then, without opening the oven door, reduce the oven temperature to 350°F. Bake for an additional 15-16 minutes.
- Remove the muffin tin from the oven and set it on a rack to cool for 10 minutes. Enjoy!
Notes
- Flour: Measure using the spoon-and-level method for best results. Too much flour can make muffins dense.
- Mixing: Stir the batter just until the flour disappears; overmixing will create tough muffins.
- Apples: Shred the apple right before adding to the batter so it stays juicy. A sweet-tart variety like Honeycrisp or Fuji works beautifully.
- Texture: For a bakery-style muffin top, sprinkle turbinado sugar over the batter before baking.
- Mini Muffins: Scoop into a mini muffin pan and bake 12-14 minutes, or until a toothpick comes out clean.
- Loaf Option: Bake in a greased 8×4-inch loaf pan at 350°F for 45-55 minutes, tenting with foil if the top browns too quickly.
- Storage: Muffins stay moist at room temp for 2-3 days, refrigerate up to 5 days, or freeze for up to 3 months. Thaw at room temperature or gently warm in the microwave.
- Serving: These are mildly sweet muffins, perfect plain, or with a spread of apple butter or nut butter.
Nutritional information is only an estimate. The accuracy of the nutritional information for any recipe on this site is not guaranteed.
When the autumn season arrives, these are the first batch of muffins I bake. The family loves them and doesn’t even know how much better-for-them they are with whole wheat flour and natural sweetening!