Healthy Apple Muffins

These healthy apple muffins are soft, moist, and packed with fresh apples, warm cinnamon, and toasted walnuts. They’re made with whole wheat flour, Greek yogurt, and naturally sweetened with pure maple syrup. Enjoy them for an easy snack, fall breakfast, or lunchbox treat!

My toddler’s favorite snack are muffins, especially these healthy apple muffins. I wanted to create something that was warm and cozy for fall, and these muffins have become a staple in our house!

I often make a batch ahead of time and freeze them for a convenient grab-and-go snack.

Why You’ll Love These Apple Muffins

They’re soft, moist, and packed with apples. There’s grated apple and chopped apples in this recipe, so every bite is loaded with juicy cinnamon-spiced apples. It’s a cozy healthy breakfast that hits the spot every time.

Made with simple ingredients. If you like to make healthy muffins, you probably already have most of what you need in your fridge or pantry.

They’re naturally sweetened. Instead of using refined sugar, these muffins are sweetened with pure maple syrup. The apples also add a touch of natural sweetness.

Easy to make. There’s no mixer required. Just mix the ingredients together, scoop the batter into a muffin pan, and let the oven do the work.

Perfect for breakfast or snacks. You can make these muffins ahead of time, which is great for busy mornings, lunchboxes, afternoon snacks, or when you need a little sweet treat to go with your coffee.  

Healthy apple muffin ingredients

Whole wheat flour: I use 100% whole wheat flour. It adds a delicious hearty flavor and wholesome texture to these pumpkin muffins.

Baking powder and baking soda: These are leavening agents that help the muffins rise, which makes them light and fluffy. It’s important to make sure your baking powder and baking soda are fresh to ensure a proper rise.

Salt: This helps balance the sweetness and enhances the flavor of the other ingredients.

Cinnamon, nutmeg, and allspice. I use a blend of warm, aromatic ground spices to bring out the natural sweetness in the apples and give these muffins a cozy, fall flavor.

Eggs: I use two eggs for this recipe which help make the muffins moist and binds the ingredients together.

Pure maple syrup: This helps to naturally sweeten the muffins without adding refined sugar.

Greek yogurt or sour cream: This helps keep the muffins moist and adds a boost of protein. I usually use 0% plain yogurt. You can use sour cream if you prefer.

Butter or coconut oil: You can use melted coconut oil or unsalted butter for this recipe. I usually use butter because it gives it better flavor.

Vanilla extract: This gives the muffins good flavor.

Grated apple: This helps make the muffins extra moist and tender. Use the large holes of a box grater to grate the apples. It will melt into the batter as it bakes, which adds a natural sweetness to the muffins.

There’s no need to squeeze out the excess water from the grated apple.

Chopped apple: Adding finely chopped apple to the muffins gives you soft, juicy apple in every bite.

I recommend cutting the apple fairly small so they become tender while the muffins bake.

Toasted walnuts: This is an optional ingredient, but it adds a nutty flavor and a little crunch that pairs well with the sweet apples and cinnamon.

Turbinado sugar: This is an optional ingredient, but it adds a lightly crip topping. Sprinkle a little of the coarse sugar on top of the muffins before baking. This gives them a bakery-style look and makes them taste extra delicious!

The best apples for apple muffins

The best apples for apple muffins are sweet or slightly tart apples that hold their shape when baked.

I tested this recipe using Gala apples, which are juicy with a soft texture after baking. Other apples I recommend using are Granny Smith, Honeycrisp, Pink Lady, or Ambrosia.

You can even combine a sweet apple like Honeycrisp with a tart apple like Granny Smith.

How to make healthy apple muffins

Preheat the oven to 425°F. Lightly grease a 12-cup standard muffin tin with butter or nonstick spray.

In a large bowl, whisk together the whole wheat flour, baking soda, baking powder, salt, cinnamon, nutmeg, and allspice.

In a medium bowl, whisk together the eggs, pure maple syrup, Greek yogurt (or sour cream if using), melted butter (or coconut oil if using), vanilla extract, and grated apple.

In a small bowl, add the chopped apple, whole wheat flour, and cinnamon. Toss to evenly coat the apples.

Make a well in the center of the dry ingredients and carefully pour the wet ingredients into the dry ingredients. Gently whisk, stir, or fold just until combined and no dry flour pockets remain. DO NOT OVERMIX. The batter will be very thick. 

Fold in the chopped apple and toasted walnuts (if using). Scoop the muffin batter into the muffin tin liners, filling them all the way to the top.

Optional Step: Sprinkle about ½-1 teaspoon of the turbinado sugar on top of each muffin.

Bake for 5 minutes at 425°F, then reduce the temperature to 350°F (without opening the oven door). Bake for an additional 13-15 minutes, or until a toothpick inserted into the center comes out clean.

These muffins should take about 18-20 minutes in total to bake. Let them cool in the pan for 5 minutes before enjoying.

Do you need to peel the apples?

No, you don’t have to peel the apples for this muffin recipe. It comes down to the texture and appearance you prefer.

I like to peel the apples for this recipe because it yields a soft, tender apple muffin. The peel can remain slightly chewy after baking, which I’m not a fan of.

How to store healthy apple muffins

Let the muffins sit in the pan for 5 minutes after baking, then transfer to a wire rack to cool completely.

Leftover apple muffins can be stored in an airtight container for up to 3 days. You may want to place a paper towel under the muffins to absorb excess moisture and prevent them from getting soggy.

Fridge: For longer storage, place them in an airtight container in the fridge for up to 5 days. Tastes best after warming them up for 10-15 seconds in the microwave.

Can you freeze apple muffins?

Yes! Allow them to cool completely, then wrap each muffin individually in plastic wrap and place them in a freezer-safe bag or container. Freeze for up to 3 months. Thaw overnight in the fridge or at room temperature.

More healthy breakfast recipes to try

• Healthy pumpkin muffins
• Healthy apple cinnamon pancakes
• Healthy pumpkin bread
• Healthy pumpkin pancakes
• Whole wheat pancakes
• Healthy banana bread
• Healthy zucchini bread

Please let me know how you like this healthy apple muffin recipe in the comments below! Your feedback and review encourages me to keep creating new and yummy recipes. I hope you love these apple muffins as much as I do.

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