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.
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
Key Ingredients & Why They Work
- 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!
- 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.
- 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.
- 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.
- 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.
- 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.
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.
Healthy Apple Muffins: Helpful Notes
- Expect a thick batter. Thick batter helps ensure the muffins lift UP rather than spread OUT.
- 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.
- 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).
- 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!
I bake muffins A LOT, usually at least once a week. They’re one of my favorite kid-friendly baking recipes and back to school 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
- Blueberry Muffins
- Healthy Blueberry Banana Muffins
- Pumpkin Crumb Cake Muffins
- Zucchini Muffins
- Apple Cinnamon Muffins (with crumb topping)
- Bran Muffins
- Or try my all-in-one Muffin Recipe
Healthy Whole Wheat Apple Muffins
- Prep Time: 10 minutes
- Cook Time: 22 minutes
- Total Time: 35 minutes
- Yield: 12 muffins
- 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
- 2 cups (260g) whole wheat flour (spooned & 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 (70g) coconut oil, melted (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
- Preheat oven to 425°F (218°C). Spray a 12-count muffin pan with nonstick spray or line with cupcake liners. Set aside.
- 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.
- 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).)
- 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.
- Muffins stay fresh covered at room temperature for a few days, then transfer to the refrigerator for up to 1 week.
Notes
- 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.
- Special Tools (affiliate links): 12-count Muffin Pan | Cupcake Liners | Glass Mixing Bowls | Whisk | Box Grater | Rubber Spatula | Cooling Rack
- 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.)
- 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).
- 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.
- 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.
- 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
I loved these muffins so badly 🙂 You are my baking master, Sally! I love your blog and works.
★★★★★
These are the best muffins I have ever cooked 🙂
Lovely flavour, moisture and texture, thanks!
★★★★★
I look forward to making this recipe! When you lower the oven temperature after the 1st 5 minutes do you leave the muffins in the oven? Or take them out until the new temperature is reached and then put them back in the oven?
Hi Cheryl, you can leave the muffins in the oven as the temperature decreases. No need to remove. Hope you enjoy the muffins!
These were delicious! Even my non-breakfast eater asked for a second. Have you ever added dried cranberries or other dried fruits? If so how much would you suggest?
★★★★★
Hi Stephanie, dried cranberries or other dried fruits would be delicious here! We’d recommend using them in place of the 3/4 cup of nuts — same amount.
Honestly was skeptical to try but with 5 stars I gave it a shot. I’m eating much healthier and want to find healthier options that taste great. I’ve always struggled with “afternoon snack time” and in the winter don’t like that most of the options available are cold vegetables. I was hoping to find a warm snack that is healthy and doesn’t break the calorie bank. Did not have coconut oil (added to my shopping list) so used vegetable oil. Also, when grating my apples they looked more like mush then the picture and gave me a lot of juice. It worked out perfectly and for two adult men who despise anything healthy (well one is almost an adult 16 and 57), they loved them!!! I came back to the site this morning to “officially” print the recipe so it doesn’t get lost as this will now be a family staple. Thank you!
★★★★★
Delicious apple flavour throughout! Turned out wonderful just the way it was written. Hearty, but still moist. Thank you!
★★★★★
Very good muffins! I used oat flour, just because I prefer it and they turned out great! This was my second time making them and I only had 1 apple so I used 1 apple and some strawberries. I also cut down on the sugar (maple syrup). I only put in about 1 teaspoon. I added extra unsweetened apple sauce (1 cup instead of 3/4 cup) and they were still moist. They were perfect and
very healthy for my toddler. 🙂 I will use this recipe from now on and try different things!
★★★★★
Could I use something other than coconut oil?
Hi Yvonne, you can use melted butter or vegetable oil instead.
These look amazing! Are you able to do these as mini muffins? Is there any change to the cooking time or temp?
Hi Ryan, For mini muffins, bake 11–14 minutes at 350°F (177°C).
Amazing. Whole family gobbled these up.
★★★★★
All I can say is YUM YUM YUM! I replaced half of the whole wheat flour with oat flour (By weight, NOT by volume), and lo and behold they turned out perfect! I have done all whole wheat before and they were amazing as well. Great recipe, thanks for sharing!
★★★★★
I don’t have applesauce on hand, could I make these with just more grated apples and maybe 1/4 olive oil to makeup for the moisture?
Hi Emily, additional apples will likely weigh down the batter and make the muffins heavy/dense. You’ll also lose a bit of flavor without the applesauce. We’d recommend waiting until you have some applesauce on hand (or using your apples to make some!) to make these muffins.
Moist and not overly sweet, turned out beautifully. I used wholemeal spelt flour which worked really well. I added 3 grated apples and used brown rice syrup instead of the maple syrup. I added the pecans which complement the apples. Made 9 muffins. You won’t be disappointed- try them yourself!
★★★★★
Thanks so much for a great recipe! I used about 3/4 wheat and 1/4 spelt and the lower amount of maple syrup. Also used veg oil since it was all I had. Made a half recipe so baked about two minutes less. Perfect!
★★★★★
So so good!! My 5 year old is pretty picky when it comes to baked goods, and she loved these. Thanks Sally for another wonderful recipe!
★★★★★
Hi, would it be possible to substitute the entire 2 cups of whole wheat flour with 1 cup of all-purpose flour + 3/4 cup whole wheat flour + 1/4 cup rolled oats? Do you think that this adjustment would work? Thanks
Hi Justina, it’s hard to say without testing ourselves. The swap with all-purpose flour will work, but the amount of oats may need some tinkering because they’re not necessarily a 1:1 swap with flour. Let us know if you decide to do any experimenting.
I didn’t have applesauce so I substituted canned pumpkin. Slightly different flavor but the texture still was great and perfectly moist. Thanks for another great recipe!
Can these be made as mini muffins?
Hi Ruth, Absolutely! For mini muffins, bake 11–14 minutes at 350°F (177°C).
I made these muffins today and they’re great, lots of flavor, not too sweet, also not a lot of calories. I only had one apple on hand so I use 1cup of grated carrots with the one apple and it turned out great. I’ll make them again with the 2 apples next time. Overall, great recipe.
★★★★
We made these and the kids loved them! I’d like some advice though as I’m very sensitive to the taste of baking powder in recipes, is there any way to adjust this to add less baking powder? I also used oat flour (homemade) instead of whole wheat as we really struggle to get whole wheat in South Africa, but the muffins were a bit too crumbly, still edible though. 🙂 Could you please give advice on substituting with oat flour, and then if I can use less baking powder or omit entirely? I substituted the whole wheat flour by weight but am thinking a little less oat flour would be better, or maybe mixing a bit of white flour and the rest oat flour? Thanks in advance 🙂
★★★★★
Hi Andil, thank you so much for giving this recipe a try. Oat flour has very different baking properties than whole wheat flour, which is likely why your muffins came out a bit crumbly. It would take some recipe testing to determine how best to make that swap, so it will take some trial and error if you want to experiment with using it in future batches. The baking powder (and baking soda) play an important role in helping the muffins to rise, so reducing it would impact that. Perhaps a different brand would not have as potent a taste in your final baked goods? Hope this helps, and thank you again!
These are delicious!!! I’ll be making these regularly in the fall. I love the toasty warm cinnamon smell while they’re baking. They’re so moist and yummy. I used 1/2 apple, & 1/2 Asian pear, then pumpkin instead of applesauce, perfect!
Super good! I did have to use 4 apples though to get close to 2 cups! And my apples were pretty wet when grated, so I only did 1/2 C of applesauce so they weren’t too wet. So yummy. Will make many times this fall. Definitely don’t leave out the pecans. Adds a great crunch
★★★★★
Hi I don’t have allspice what can I use or is it fine to leave it out thx
Hi Trish! You can leave it out or add extra cinnamon in its place.
Wow! These are delicious! I followed the recipe to a T and they turned out amazing! Will put these in the kids school lunches and will definitely save this recipe and make over and over again.
★★★★★
I’m excited to try this recipe! I don’t have maple syrup or honey though, could I substitute dark brown sugar? If not I will hold off on these until I get groceries 🙂
Hi Charles, yes, that swap should work just fine. Hope you enjoy the muffins!
These were delicious! I made a batch for Sunday brunch. So happy there are leftovers for school lunches too!!
★★★★★
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!
★★★★★
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!!
★★★★★
Can the maple syrup be replaced with pure honey?
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).
Thank you! 🙂
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?
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!
Very good muffins! I used oat flour, just because I prefer it and they turned out great! This was my second time making them and I only had 1 apple so I used 1 apple and some strawberries. I also cut down on the sugar (maple syrup). I only put in about 1 teaspoon. I added extra unsweetened apple sauce (1 cup instead of 3/4 cup) and they were still moist. They were perfect and
very healthy for my toddler. 🙂 I will use this recipe from now on and try different things!
These look amazing! One question though… Could I substitute the applesauce with plain yogurt?
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.