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This recipe for hearty, healthy apple muffins has lived on my website since 2016. I’ve made a couple slight changes over the years so they rise taller and have a stronger apple flavor. They’re wonderfully wholesome and soft, and you’ll appreciate that they’re made without any refined sugar. These are my go-to choice when I’m looking for a quick and easy healthy muffin!

For a classic and indulgent version, try my apple cinnamon muffins.

stack of two healthy apple muffins sitting on wire cooling rack.

Today’s muffins are adapted from my morning glory muffins, which have all sorts of goodies packed inside like grated apple, grated carrot, raisins, nuts, etc. Think: carrot cake, but lightened-up.

For this apple version, we’re leaving out the grated carrot and switching up a couple other ingredients. To keep them on the lighter side, I use a mix of applesauce and melted coconut oil. This way the muffins keep their moist, rich texture but aren’t weighed down with fat.

Here’s Why You’ll Love These Healthy Apple Muffins

  • Quick and easy
  • No mixer required
  • Zero refined sugar—use pure maple syrup and apples to sweeten
  • Use whole wheat flour for hearty, wholesome flavor
  • Flavored with cinnamon, allspice, and lots of apples and applesauce
  • Absolutely healthy, but they don’t taste like cardboard (not at all bland!)
  • Dairy-free recipe
apple muffin split in half with butter melting on top.

Key Ingredients & Why They Work

  1. Whole Wheat Flour: I love using whole wheat flour in baking when I can. Whole wheat flour can quickly dry out your baked goods, so it’s important to pay close attention to the wet ingredients. For example, there’s extra butter and milk in these whole wheat dinner rolls to make up for the hearty flour. Today’s muffins are super moist and we have the following listed ingredients to thank!
  2. Eggs: This recipe used to call for 3 eggs, which weighed the muffins down and provided too much eggy structure. I updated the recipe so you use 2 eggs and more applesauce.
  3. Unsweetened Applesauce: Just as if you were making applesauce muffins, make sure you use unsweetened applesauce here. If all you have is sweetened, slightly reduce the maple syrup as noted in the recipe Note below.
  4. Pure Maple Syrup: Pure maple syrup sweetens the muffins and adds some moisture. The darker the pure maple syrup, the stronger the flavor. So if your maple syrup is extra dark with robust flavor, slightly reduce to 1/2 cup (120ml). If your maple syrup is golden or light amber colored (not very dark), use 2/3 cup as instructed below.
  5. Coconut Oil: Instead of butter or vegetable oil, use melted coconut oil. This is one of my very favorite ingredients in the kitchen and you can use it again for these chocolate banana muffins.
  6. Shredded Apples: Use shredded apples instead of chunks. Why? Shredded apples act as a wet ingredient while chunks act as an add-in. You want MOISTURE, so grab a grater just as if you were going to shred carrots for carrot cake or zucchini for zucchini bread.

You also need cinnamon, allspice, baking soda, baking powder, and vanilla extract. Chopped pecans or walnuts are optional, but add a little extra texture and flavor.

whole wheat flour, coconut oil, maple syrup, pecans, apples, and other ingredients on marble cutting board.

Today’s muffin batter comes together in just 5–10 minutes with simple kitchen tools including a couple bowls, a whisk, and a muffin pan. If you’re looking for grater recommendations, I love this box grater because it’s easy to use and has held up well with regular use. If you want to make muffins with apple chunks, try apple cinnamon bread or these equally healthful apple cinnamon baked oatmeal cups instead.

Best Apples to Use

You need about 2 cups of shredded apples, which is about 210g or 2 peeled apples. Feel free to leave the peel on if desired. The best apples to use in these healthy apple muffins are a sweet variety like Pink Lady, Honey Crisp, or Fuji. Or you can use 1 tart apple like Granny Smith and 1 sweet. A combination of flavor profiles can be important in baked goods, especially apple pie or apple crisp.

shredded red and green apple on white cutting board.

Healthy Apple Muffins: Helpful Notes

  1. Expect a thick batter. Thick batter helps ensure the muffins lift UP rather than spread OUT.
  2. Feel free to replace the allspice with nutmeg. Allspice is one of my favorite spices to use in baking and you can see it used in these peach muffins and these apple hand pies. If you don’t have allspice, don’t worry about it—use nutmeg instead.
  3. Add an optional coarse sugar topping. You can use coconut sugar, something like Sugar in the Raw, or sparkling coarse sugar (usually sold as sprinkles).
  4. Bake at an initially high oven temperature. Bake the muffins for 5 minutes in a very hot oven. Then, keeping the muffins in the oven, lower the oven temperature. This initial high oven temperature quickly lifts up the muffin top. Once the temperature is lowered, the centers of the muffins bake. I do this in all my muffin recipes.

Again, expect a thick batter. You might think you’re doing something wrong but you’re not. This batter is extra thick and that’s expected!

apple muffins batter in glass bowl and shown again in lined muffin pan.
12 healthy apple muffins on wire cooling rack with coarse sugar sprinkled on top of each.
healthy apple muffin with pecans cut in half to show center.

I bake muffins A LOT, usually at least once a week. They’re one of my favorite kid-friendly baking recipes (easy to mix & quick to bake) and they freeze wonderfully. Banana muffins are a top choice, but these healthy apple muffins come in a close second; kids and adults LOVE them.

If you need a recommendation, this muffin pan has held up well with very regular use.

Even More Muffin Recipes

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stack of two healthy apple muffins sitting on wire cooling rack.

Healthy Whole Wheat Apple Muffins

  • Author: Sally
  • Prep Time: 10 minutes
  • Cook Time: 22 minutes
  • Total Time: 35 minutes
  • Yield: 12 muffins 1x
  • Category: Muffins
  • Method: Baking
  • Cuisine: American

Description

These simple and healthy whole wheat apple muffins come together quickly. Feel free to skip the optional nuts and make sure to use shredded apple instead of chopped apple.


Ingredients

Scale
  • 2 cups (260g) whole wheat flour (spoon & leveled)
  • 1 teaspoon baking powder
  • 1 teaspoon baking soda
  • 2 teaspoons ground cinnamon
  • 1/2 teaspoon ground allspice
  • 1/2 teaspoon salt
  • 2 large eggs, at room temperature
  • 3/4 cup (133g) smooth unsweetened applesauce, at room temperature
  • 2/3 cup (160ml) pure maple syrup, at room temperature
  • 1/3 cup (80ml) melted coconut oil (or vegetable oil or melted butter)
  • 1 and 1/2 teaspoons pure vanilla extract
  • 2 cups (210g) shredded/grated apple (about 2 peeled apples)*
  • optional: 3/4 cup (about 90g) chopped pecans or walnuts
  • optional: 1 Tablespoon coarse sugar for sprinkling on top

Instructions

  1. Preheat oven to 425°F (218°C). Spray a 12-count muffin pan with nonstick spray or line with cupcake liners. Set aside.
  2. In a large bowl, whisk the flour, baking powder, baking soda, cinnamon, allspice, and salt together until combined. Set aside. In a medium bowl, whisk the eggs, applesauce, maple syrup, oil, and vanilla together until combined. Pour the wet ingredients into the dry ingredients, stir a few times, and then add the shredded apple and pecans/walnuts. With a spatula, fold everything together gently just until combined. The batter will be very thick.
  3. Spoon the batter into liners, filling them all the way to the top. If using, sprinkle tops evenly with coarse sugar. Bake for 5 minutes at 425°F, then, keeping the muffins in the oven, reduce the oven temperature to 350°F (177°C). Bake for an additional 16–18 minutes or until a toothpick inserted in the center comes out clean. The total time these muffins take in the oven is about 21–23 minutes. (For mini muffins, bake 11–14 minutes at 350°F (177°C).)
  4. Allow the muffins to cool for 5 minutes in the muffin pan, and then transfer to a wire rack to continue cooling, or enjoy warm.
  5. Muffins stay fresh covered at room temperature for a few days, then transfer to the refrigerator for up to 1 week.

Notes

  1. Freezing Instructions: For longer storage, freeze the muffins for up to 3 months. Thaw overnight in the refrigerator, then heat up in the microwave if desired.
  2. Whole Wheat Flour: If you don’t have whole wheat flour, you can replace with the same amount of all-purpose flour. My team and I have not tested this recipe with gluten-free flour, but here are some gluten-free blueberry muffins you might enjoy instead. (Feel free to replace blueberries with chopped apple.)
  3. Maple Syrup: For best results, use pure maple syrup, not breakfast syrup. The darker the pure maple syrup, the stronger the flavor. So if your maple syrup is extra dark with robust flavor, slightly reduce to 1/2 cup (120ml). If your maple syrup is golden or light amber colored (not very dark), use 2/3 cup as instructed. You can substitute honey if needed, but reduce the honey to 1/2 cup (170g).
  4. Shredded vs. Chopped Apples: It’s best to use shredded/grated apples in this muffin recipe because they work as a wet ingredient. I do not recommend chopping them instead. Feel free to peel the apples before shredding or leave the peels on—doesn’t matter either way.
  5. Why the initial high oven temperature? Like I do for most muffin recipes, bake the muffins for 5 minutes at a very hot temperature. Then, keeping the muffins in the oven, switch to a lower temperature for the remaining bake time. This initial high temperature will quickly lift the muffin tops so they’re extra high, then the centers will bake during the lower temperature bake time. This trick makes beautiful bakery-style muffins every time.
  6. Nutrition Information: Using SparkRecipes calculator, these muffins come out to 195 calories, 7.5g fat, 30g carbs each.

Keywords: healthy apple muffins, whole wheat apple muffins

Reader Questions and Reviews

  1. These look amazing! One question though… Could I substitute the applesauce with plain yogurt?

    1. Hi Didi, you could substitute some of the applesauce with plain yogurt, but I wouldn’t swap all of it. You’ll lose a lot of flavor.

  2. My son was recently diagnoses with a gluten sensitivity. Am I able to sub gluten free flour for whole wheat flour? With baking in general am I able just to swap out whatever flour and use gluten free?

    1. Hi Kristi, We haven’t tested this recipe with gluten free flours, but some readers have reported success using 1:1 flour substitutes (like Cup4Cup). If you try it, let us know how it goes!

    1. Hi Dawn, Honey is a great substitute for the maple syrup. See recipe note. You can substitute honey if needed, but reduce the honey to 1/2 cup (170g).

  3. These are amazing! I used one cup whole wheat flour and one cup AP flour. Only half a cup of syrup and added cinnamon chips, the whole family loved them!!

  4. These muffins are absolutely amazing! We picked apples this weekend and made some applesauce in the crockpot. We used that applesauce in the muffins. I used melted butter instead of coconut oil. My 7 year old daughter said they taste like September!

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