These Healthy Apple Muffins are made with whole wheat flour, applesauce, grated apples and warm fall spices. Better yet, they are easy, moist and fluffy!

Can’t get enough apple desserts for healthy snacks? Then you’ll probably love healthy apple bread too!

Three healthy apple muffins stacked on top of each other. Apples, cinnamon sticks and napkin on a counter.

With fall in full swing, I can’t wait to harvest the apples from our apple tree! Then make tons of Instant Pot applesauce and bake multiple batches of these healthy apple muffins.

Healthy baked apples are so good and so easy, too!

This recipe dates back to 2014. I have made it easier to make sweetened with maple syrup and switched chopped apples to grated apples.

The result is more moist muffin with a prominent apple flavor. And no blender or mixer needed like before.

Apple muffins, apples and towel on a counter.

Why You Will Love These Healthy Apple Muffins

  • Easy to make: One bowl and 35 minutes.
  • Simple ingredients: If you have on hand two apples, you probably can make these muffins today.
  • Freezer friendly: Make a few batches and freeze for busy back-to-school and work mornings.

Key Ingredients and Notes

Whole wheat flour, apples, oil, maple syrup, applesauce, vanilla extract, walnuts, eggs, cinnamon, nutmeg, baking powder, baking soda, salt.
  • Flour: You can use regular whole wheat flour, spelt flour, whole wheat pastry flour or white whole wheat flour. We have not tested recipe with all-purpose flour or gluten free flour.
  • Applesauce: Use unsweetened applesauce. Often I use Instant Pot applesauce. In a pinch, it can be replaced with plain yogurt.
  • Apples: You can use any sweet apple variety like Honeycrisp, Fuji, Pink Lady or Gala. You can also use one sweet apple and one tart apple like Granny Smith. Grated is better than chopped, and it’s up to you if you want to peel it or not.
  • Oil: I recommend using avocado oil or coconut oil for the healthiest results. However, any neutral oil like light olive oil or grapeseed oil would work.
  • Eggs: Use two large eggs. I have not tested but possibly you could make muffins vegan with flax eggs or chia eggs.
  • Maple syrup: I like the taste, texture and moisture maple syrup adds to the muffins. Dark maple syrup is fine too. Honey would also be great. Also agave nectar. Note sweetener has to be liquid and not dry.

How to Make Healthy Apple Muffins

Making healthy apple muffins is extremely easy in one bowl!

Liquid ingredients and spices whisked in glass bowl and blue whisk.

Combine wet ingredients: Grab a large mixing bowl. Add eggs, applesauce, maple syrup, oil, vanilla extract, cinnamon, nutmeg, baking powder, baking soda, and salt.

Whisk well to combine, making sure baking powder and soda are dissolved. No white lumps are visible.

Muffin batter in a bowl with spatula.

Add flour: Stir gently and do not over mix. The best way is to give a few stirs and when a few white patches of flour are left, leave the batter sit for a minute or two.

Flour will absorb the moisture of liquid ingredients.

Grated apples on white plate, box grater and two apple cores on a counter.

Grate apples: Grate apples on large holes of a box grater.

Chopped walnuts, grated apples, muffin batter in a bowl with spatula.

Add apples and walnuts: Chopped walnuts or pecans are optional but add nice texture and flavor. Grated apples add moisture. Stir them in just until combined.

Unbaked muffin batter in dark muffin tin.

Bake muffins: Divide the batter between the muffin tray. Cups will be very full but should not spread as batter is quite thick.

Bake for 23 minutes or until a toothpick inserted in the center comes out mostly clean. With a few crumbs is fine but not wet.

Baked healthy apple muffins sprinkled with sugar in muffin tin. Towel, apples and cinnamon sticks on a counter.

Allow to cool: Then, remove them from the oven and allow them to cool for 5 minutes before transferring to a wire rack to finish cooling. Or enjoy warm!

What Are The Best Apples to Use?

The truth is you can use any apple in baking.

For this healthy apple muffin recipe, I recommend to use any sweet variety like Honeycrisp, Fuji, Pink Lady or Gala apples. Apple varieties differ by geographic regions as well. So if you have some sweet apples not listed here go ahead and use them.

You can also combine one tart and one sweet apple, that’s what I did. To peel or not to peel is a personal choice. Apple skin bakes and becomes soft.

Expert Tips

  • Make sure to use the spoon and level method: When measuring the flour rather than scooping the cup directly into the flour bag), spoon the flour into the cup, then level with a knife.
  • Be careful not to overmix the batter: Otherwise, the gluten in the flour can become overworked, and you’ll end up with tough, stodgy whole wheat apple muffins.
  • Muffin tin will be quite full: It might look like too much batter in each opening but muffins should not spread.
  • For mini muffins: I recommend checking on the mini muffins at 12-14 minutes.
  • Optional sugar topping: You can sprinkle muffins before or after baking with coarse white sugar.
One apple muffin sliced in half with butter. More muffins, green apple, napkin on a counter around it.

How to Store and Freeze

Storing: Transfer cooled muffins to an airtight container and store them in a cool dry place for up to 3 – 4 days or in a fridge for up to a week.

Freezing: Place the cooled muffins in an airtight container with parchment paper between the layers of muffins and freeze for up to 3 months. When you want one, allow it to thaw in the fridge overnight or heat from frozen.

FAQs

What are the best apples for muffins?

Make sure to use a sweet variety. You could use Fuji, Pink Lady, Honeycrisp, Red Delicious or Gala apples. You can use one sweet and one tart apple like Granny Smith or McIntosh.

My apple muffins seem undercooked?

If you followed the recipe it shouldn’t happen. The best way to test if the muffins are ready is to insert a toothpick into the center. If it comes out with a few crumbs, it’s fine. But it shouldn’t be wet at all. If it is, continue baking for a further few minutes.

Can I omit the oil and increase the applesauce?

No. Without any fat muffins will come out rubbery.

How do I make these muffins gluten-free?

I have not tested this recipe with gluten free flour. You can try my almond flour blueberry muffins and replace blueberries with grated apples.

More Healthy Apple Recipes

More Healthy Muffin Recipes

You can also browse through a complete list of my muffins recipes!

Nine healthy apple muffins sprinkled with sugar. One muffin unwrapped in the center. Decor around.
Three healthy apple muffins stacked on top of each other. Apples, cinnamon sticks and napkin on a counter.

Healthy Apple Muffins

These Healthy Apple Muffins are made with whole wheat flour, applesauce, grated apples and warm fall spices.
5 from 11 votes
Servings 12 muffins
Calories 244
Diet Low Fat
Diet Low Fat
Prep Time 12 minutes
Cook Time 23 minutes
Total Time 35 minutes

Ingredients 
 

Instructions 

  • Preheat oven to 350 degrees F and line muffin tin with parchment paper liners and spray with cooking spray. Set aside.
  • In a large mixing bowl, add eggs, applesauce, maple syrup, oil, vanilla extract, cinnamon, nutmeg, baking powder, baking soda, and salt. Whisk well to combine, making sure baking powder and soda are dissolved. Add flour and stir gently to mix. Do not over mix.
  • Add grated apples and walnuts, give a few stirs just until combined.
  • Using large ice cream scoop, fill 12 tin openings with batter. They will be very full. Bake for 23 minutes or until toothpick inserted in the middle comes out clean.
  • Remove from the oven, let muffins cool in the tin for 5 minutes and then transfer to a cooling rack to cool more, or enjoy warm.

Notes

  • Store: Store in an airtight container in a cool dry place for up to 3 – 4 days or in a fridge for up to a week.
  • Freeze: Bake and cool muffins completely. Arrange in a single layer in resealable plastic bag or any container with a lid. Freeze for up to 3 months.
  • Apples: Bets apples to use are any sweet variety like Honeycrisp, Fuji, Pink Lady or Gala apples work. You can also use one sweet apple and one tart apple like Granny Smith. Grated is better than chopped, and it’s up to you if you want to peel it or not.
  • Other flours: You may also use whole wheat pastry flour or white whole wheat flour. I have not tested it with gluten free flour, so can’t tell. You can try my almond flour blueberry muffins and replace blueberries with grated apple.
  • Other add-ins: Up to a 1/2 cup of chocolate chips, dried cranberries or raisins.

Nutrition

Serving: 1muffin | Calories: 244kcal | Carbohydrates: 39g | Protein: 5g | Fat: 9g | Saturated Fat: 1g | Trans Fat: 0.003g | Cholesterol: 27mg | Sodium: 236mg | Fiber: 4g | Sugar: 19g
Course: Breakfast, Snack
Cuisine: North American
Author: Olena Osipov
Did you make this recipe?Mention @ifoodreal or tag #ifoodreal!

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About Olena

Welcome! I grew up in Ukraine watching my grandma cook with simple ingredients. I have spent the last 11 years making it my mission to help you cook quick and easy meals for your family!

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Comments

  1. Did you just modify the recipe? I have a copy of this recipe with Medjool dates in it? Can you repost it? I didn’t copy the instructions thinking it would be here.

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