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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 and this muffin pan have both 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. Muffins came out So good. Flavour and smell was awesome. Definitely will make again. Thanks Sally for sharing really good recipe..

    1. Sally, Huge fan of yours. Could I make this in mini loaf pans? Apples are a staple of the Jewish new year and would love to gift these in the form of mini loaves. Would I just adjust the time?

      1. Hi Judith, absolutely — what a great idea! We’re unsure of the exact bake time, as it will vary based on the size of your mini loaf pans. Keep a close eye on them and use a toothpick to test for doneness. No other changes necessary.

  2. This has been my standby whole wheat muffin recipe. I use 1.5 cups of white whole wheat flour and a half cup of oat flour made by processing rolled oats in my mini food processor. They always come very moist and delicious. Id like to try adding a little streusel topping before baking. Will that work?

    1. Hi Judy, you can do either — it won’t make a difference in the recipe either way. Enjoy!

    2. Hi Sally,
      What’s the substitute for
      Maple syrup? Where
      I live – Indonesia- Maple syrup is hard to find and if there is any its very expensive

      1. Hi Sarah! I’m glad to help. Honey is a great substitute. See recipe note. You can substitute honey if needed, but reduce the honey to 1/2 cup (170g).

  3. Hi Sally…I’m wondering if I can omit the oil and just increase the applesauce?
    Thanks!

    1. Hi Linda, Without any fat, the muffins will have a rubbery texture. We don’t recommend replacing the oil altogether.

  4. Made two batches of these. Recipe was easy to follow. Didn’t add any nuts as I didn’t have any. Very happy with the recipe, thank you!!

  5. These were delicious! Thank you for sharing this recipe! Next time I would like to use the Jumbo muffins tins- do you recommend I keep the temps the same, just that I cook it longer at 350?
    Thanks!

    1. Hi Kristin! For jumbo muffins, bake at 425°F for 5 minutes, then, keeping the muffins in the oven, reduce the oven temperature to 350°F (177°C) and continue to bake for 25-26 minutes until the tops are lightly golden brown and centers are set. Use a toothpick to test. Enjoy!

  6. What a great recipe! I’m a guy who has never baked but love baked goods. Too much, lol! So I made these with whole wheat flour, no sugar or syrup or honey, just sweetness from applesauce, raisins, apples, and I add a grated carrot. Spectacular! have been making them almost weekly. Today switched up and made banana walnut. Next week orange cranberry. I feel so empowered, lol! It’s so flexible and forgiving. I also hate those sprays so I followed a neighbor’s advice and just wet the muffin pan with water. Brilliant! They slipped right out and clean-up was a snap. She said she learned this trick from a french chef. Thank you so much for helping me find a great healthy snack.

    1. Hi Jeff – your changes sound great for my dietary needs. What did you sub for the maple syrup to make up for the lost wetness of the batter? And thanks, Sally, for a luscious, healthy muffin recipe?
      !

    2. Love your swaps! I find using maple syrup for anything but pancakes a waste of an expensive sweetener, and I love you went free of added sweeteners. Raisins I’m sure added a punch of sweetness. I’m going to try this with olive oil instead of coconut to avoid the saturated fat.

  7. These muffins are absolutely delicious! Thanks so much for sharing, these will be a weekly treat in my house!

  8. I made these muffins with my 3 year old granddaughter and they were a big hit! I omitted the nuts for an equal amount of raisins. I was skeptical about using whole wheat flour but they were moist and tender. They kept wonderfully in an airtight container for several days and reheated them on subsequent mornings in the microwave for about 30 seconds. These healthy, scrumptious muffins have become a staple in my breakfast recipes! Great for an afternoon snack, too.

    1. Hi Sally and team.
      I absolutely love ur recipes. Ur my go to girl for baked goods. Ur tips n tricks are fantastic. Chewy choc chip cookies and apple hand pies are our family favourites, among others. I’ve been able to share many recipes and ur site to soooo many family, friends and work colleagues. U inspire me to bake more so thank u very much.
      So my question is about the apple sauce. Can I use home made apple sauce? Or substitute for something else or even omit it from the recipe. Kind regards to you and ur team from down under. Rock on Aussies

      1. Hi Caz, thank you so much for making and trusting our recipes! You can definitely use homemade apple sauce in this recipe — same amount. Hope you love the muffins!

    1. Hi Katie, the flavor will be different, but olive oil will work!

  9. These are FANTASTIC! Super easy and SO flavourful! Sally has done it again! 🙂

  10. Firstly – this recipe was absolutely delicious, so happy I tried it! The muffins were a huge hit with my family, including with my partner – who is not even an apple fan!

    What would your recommendation be if I wanted to replace all of the maple syrup with brown sugar? I’m wondering if I can add some greek yogurt to add moisture back in, and if I can, how much you’d recommend.

    Thanks!

    1. Hi Vicky, so glad you loved these muffins! That swap would require some testing, but it sounds like you’re on the right track. Let us know what you try!

    2. The simple answer is you would use 130g or 2/3 cup sugar (white or brown doesn’t matter) and 78ml or 1/3 cup liquid (water, milk, Greek yoghurt, single/natural yoghurt, applesauce, mashed banana, pumpkin purée all works in baking (despite how much liquid is in the product vs protein and fibre) . For reference, I know my maths is correct, that it works in reality rather than just merely theory 🙂

    3. More detail, the maths-y answer: I have found a ratio that works to replace maple syrup/honey with dry sugar and additional liquid (or vice versa) based on total sugar in maple syrup vs sugar, and assuming that rest of the maple syrup weight that isn’t made up of sugar is water for the maths. So for this recipe 2/3 cup maple syrup = 208g, of which 130g is sugar and 78g is water (but in reality I use milk for more flavour). Forgot to write the ratio is 40g honey or maple syrup has the same amount of sugar as 25g dry sugar.

    1. Hi Liz, For mini muffins, bake 11–14 minutes at 350°F (177°C).

  11. Do you think that I could substitute almond flour for whole wheat? Sounds great but my husband has diabetes and we’re trying to go low carb.

  12. This recipe sounds yummy. If we eat gluten-free, what is the best gf flour substitute for this recipe? oat flour? almond flour? 1:1 flour substitute?

    1. Hi Misty! 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!

  13. Hi Sally! I love your baked oatmeal cups and I have tried a few variations! It transformed me into a baked oatmeal enthusiast! I saw you updated this recipe and it looks amazing and I would love to try it. I was wondering what the difference is between this recipe and your simply applesauce muffins? I saw that those have oats in it which I love, but this one seems like it is a little bit sweeter which would fit with my sweet tooth. I am looking for something less cake-like and more breakfast / muffin-like. Do you have recommendations?

    1. Hi Miriam, the recipes are pretty similar, but these are a little heartier with more texture from the shredded apple. From your description, it sounds like this recipe is the best choice!

  14. Great recipe! I added chopped walnuts and made them in mini size. Baked to perfection in 12 mins. What a winner! Thank you Sally. I will serve these for breakfast tomorrow and then add to school lunches when school starts next week. Thanks again!

  15. I just made these for the first time, and they taste wonderful. I made them with gluten free flour as my husband has celiac disease. That is the only change I made to the recipe. Nobody would know they were gluten free unless I told them.

  16. Hi Sally, I was wondering if I can substitute whole wheat flour with oat flour? if so, do you know how many grams do 2 cups of oat flour, properly measured, should weigh? Thank you!

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

  17. I accidentally added the apples to the wet batter before mixing it in with the dry ingredients. Will that change anything?

    1. Hi Susan, it may be a bit more difficult to fully mix in the dry ingredients, but just be careful not to over mix. Hope you enjoy the muffins!

  18. These are so delicious! I used 1/2 oat flour and 1/2 regular flour, as I didn’t have whole wheat on hand. They came out soft, moist, yummy, and the trick of baking for five minutes at a higher temp, then lowering, indeed produced nice high tops. Thank you for yet another amazing recipe!

  19. Hi Sally! Can you use white whole wheat flour or whole wheat pastry flour instead of regular whole wheat? What is the difference between these 3 flours?

    1. White whole wheat flour is just a type of wheat. It’s 100% whole wheat, just made from hard white wheat berries (that’s what I learned from King Arthur Baking’s website!). Whole wheat pastry flour is finer and (I think!) has a lower protein content. I would look it up online for a more in-depth look at the differences. You could use either in this recipe.

  20. These are very good. The batter is easy to work with. If you substitute honey for the maple syrup I recommend adding more Allspice (or Maple flavoring). The honey does not impart as much flavor as the Maple syrup would have.

  21. Hi Sally’s! Does the nutritional analysis for this recipe include the optional nuts and coarse sugar on top? I am guessing not.

    1. Thank you Lysa! Shredded apples are important in this batter because they act as a dry ingredient. If you’d really like to chop them, I would add a little more liquid to the batter, such as some milk.

  22. Oh Sally! These are perfect! I loved that they were delicately sweet as opposed to a muffin that gives a sugar rush. I did change 1 thing however, I reduced the maple syrup to 1/3C and added a 1/3C of King Arthur’s Boiled Cider for more apple flavor. I also up the “healthy” part of these muffins by throwing in a 1/4C of chia seeds and 1/4C ground flax seed. These have earned a spot on my rotation.

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