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.
I originally published this recipe in 2016 and have since added new photos, a video tutorial, and a few more success tips.
One reader, Eileen, commented: “These muffins are as delicious as they are beautiful… and they’re healthy!… The way the tops rose up was amazing! I will be making these often. ★★★★★“
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 has 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 (180g) 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 silicone 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 | Silicone 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.
Reader Comments and Reviews
These muffins are great! I decided to grind my wheat right them and it made it extra yummy, I think. I didn’t have any apple sauce and wasn’t sure what to do. I finally decided I only had some 4 berry jelly, so I used that and it worked perfectly. I did add raisins as I love them with the walnuts. Both husband and son loved them also. I actually added a scoop of vanilla protein powder too. So yummy.
These are amazing… you can’t tell that there is no refined sugar. I subbed pumpkin puree for the apple sauce and they turned out great. I also peeled and chopped the apples into small pieces and cooked them on the stove with 2 tablespoons apple cider vinegar and some cinnamon until the apples softened. I highly recommend this!! The apples are a naturally sweet addition each time you bite into them and they are the perfect soft texture along with the muffin. Something different to try that turned out really good!
Wondering if this could be made into a loaf instead of muffins.
Hi Laura, absolutely. This batter will fit in one 9×5-inch loaf pan. You can bake at 350 degrees, but we’re unsure of the exact bake time. Keep a close eye on it and use a toothpick to test for doneness. Enjoy!
Can I use whole wheat pastry flour instead?
Hi Cindy, that should work in a pinch. The muffins will be more soft and delicate.
These muffins were so delicious and my family really liked them! I couldn’t wait for fall treats so I made these in the summer! I used apples from my family’s apple tree also! I used a sweetened apple sauce then only 1/3 cup of date sugar instead of 2/3 cup of maple syrup and they were sweet and moist enough. Thank you, Sally!! It’s a keeper recipe!
We’re so glad you loved this recipe, Sam!
Love these muffins! Not rubbery or dry. Today, I substituted the fruit sauce for oat yoghurt, and the coconut oil for canola oil (less saturated fat). Still delicious
Very good muffins except for one thing. Too much cinnamon. It overpowers the apple flavor. Can’t taste the apples at all.
Very good muffins except for one thing. Too much cinnamon. It overpowers the apple flavor. Can’t taste the apples at all.
Can this be doubled
Hi Lynn, for best results, we recommend making separate batches rather than doubling.
Hi Sally
I am a hugeee fan for starters 🙂
I have a question, I like in Turkey and we don’t have applesauce here. What can I use as alternative? Similarly, maple syrup also isn’t so easy/cheap to find.
Thank you and happy baking
Hi Ruba! You can substitute honey for the maple syrup, but reduce the honey to 1/2 cup (170g). Applesauce is a pretty key ingredient here, but you could try replacing the applesauce with the same amount of pumpkin puree or mashed bananas, for a different flavor.
Couldn’t she just make her own Apple Sauce? I make mine all of the time! And it’s much better than store bought.
Making applesauce is very easy. Peel and core 4 large apples add
0.5 cup water 1. tsp lemon juice. I don’t use any sugar. Cook until apples are soft. Use a potato masher and mash to the consistency that you like.
Thanks for sharing how you make your homemade applesauce. I’m going to try making some instead of buying jarred applesauce.
These were very easy to make and tasty. My 1 year old loved them and my husband (who says he “hates fruit in baked goods”) finally tried one and admitted it was very good. I used silicone liners in my muffin pan and I think they took longer to cook all the way. Next time will try baking them in the tin without liners
My family loves these muffins. I make the mini version every other week (we alternate with your mini cornbread muffins, so good too!!) and they’re the best school snacks and lunch treat. We run out every time!
I was curious if this could be made into a cake or if there’s another low sugar cake you could recommend? My mother is diabetic and I’d love to make her something special, and thought something like this would be a great alternative to a traditional birthday cake. Sally is always my go to for birthday cakes but unfortunately the chocolate chip cake (amazing!!!) and piñata cake (show stopper!!!) are just a bit too sweet for this celebration. Thanks again for all your great recipes!
Hi Lisa, we’re so glad these are a favorite! This amount of batter would fit well in a 9×5-inch loaf pan, although we’re unsure of the exact bake time. You could also use this Cake Pan Sizes and Conversions guide to scale for another size pan. Or, you can read about how Sally modified her banana muffins for a small cake in this post. Hope this helps!
Sally, you never disappoint. I am trying to find GOOD healthy options for my kids and this one is a winner. I did not include the optional sugar on top and they were still really good. The kids would have liked something a bit sweeter, so I see the purpose in it. But for an every day, afterschool snack – this is a good one!
Oh my gosh! I made these muffins yesterday with King Arthur unbleached flour. They were fantastic! I will be making them often. Thanks, Sally.
How long does applesauce take to reach room temperature? Mine is store bought and unsweetened
Can I replace the maple syrup with honey? Thanks!
Hi Keri, yes, same amount. Enjoy!
Sally McKenney,
I love thought I’d give this a go GREAT.
These healthy apple muffins are delicious! After getting all my ingredients together I realized I didn’t have applesauce nor enough WW flour, so….I used my homemade apple butter and used half WW flour and half spelt flour. The rest of the recipe I followed as written. In spite of having 2 substitutions, these healthy muffins are moist, great tasting and rose beautifully! Baking at 425 degrees for 5 minutes – and 350 degrees for 16 min. is genius…I will bake all my muffins this way from now on. Thank you Sally and team for this great recipe – a great step towards MAHA!
Delicious and extremely easy to make. I made them gluten free and they are so moist.
Thanks for another perfect recipe.
This recipe was great! I have some gastro issues and I’m avoiding refined sugar and regular flour. These not only were healthy but extra delicious. My family and I loved them! If possible, do you have nutritional facts on these?
Again thanks for a recipe that will be a keeper in our family!
Hi Pam, so glad you enjoyed these! We don’t usually include nutrition information as it can vary between different brands of the same ingredients. Plus, many recipes have ingredient substitutions or optional ingredients listed. However, there are many handy online calculators where you can plug in and customize your exact ingredients/brands. Readers have found this one especially helpful: https://www.verywellfit.com/recipe-nutrition-analyzer-4157076
Hello Sally,
Another winner!
I want you to know how much I appreciate your careful development of recipes, with lots of testing, so that your readers can just breeze in and have success the first time! I have recommended your site many times.
Some time ago, you told an entrepreneur that she could use your recipes in her new restaurant. I have a different kind of commercial request.
I write murder mysteries, circling around a mechanic, a chef, and their friends, including a baker. Recipes are part of the content. If I give you credit, could I use some of your recipes?
Hi K, We are glad you enjoyed the muffins and thank you for the kind comment! Can you send this request to our email sally@sallysbakingaddiction.com?
We loved these! So moist! I can’t believe there is no refined sugar in these and just pure maple syrup which adds just the right amount of sweetness. We’ll make again!
My mini muffins turned out great, even though I forgot to lower the temp 5 minutes in! I was so focused on resetting the timer and figuring out times since I had both mini muffins and a few regular muffins in there, I just totally spaced on changing the temp! I didn’t even notice until I checked the regular muffins and noticed they were getting a little dark. Either way, they taste delicious! I used honeycrisp apples. I also subbed a little of the whole wheat flour with one scoop of vanilla cinnamon protein powder.
Can you substitute oat flour instead of whole wheat?
Hi Merri, we haven’t tested this recipe with oat flour. It’s not always a 1:1 swap, so it would take a bit of experimenting to properly incorporate into this recipe. For best taste and texture, we recommend sticking with the recipe as written. Hope you enjoy it if you give it a try!
We love this recipe! We make it with Einkorn wheat and they are absolutely delicious!!! I make them all the time now!!! Thank you for sharing it!! My husband, children, and grandchildren love them! We will be trying your Morning Glory muffins soon! I was so glad to find this recipe and try it! Thank you again!!! It has become one of our family favorites! I would give 10 stars if I could!
These are moist and wonderfully delicious . The high temp for 5 minutes is perfect as the muffins puff up nicely. I used a combo of wheat and white flour and 2 tbs of coconut flour. I also used 1/3 cup of real maple syrup and 1/4 cup of honey. I like that these are somewhat healthy and have more natural ingredients. Thanks!
Looks yummy and healthy! What does maple syrup do, only adding sweetness? Could it be omitted? Thank you!
Hi Natalia, we don’t recommend totally leaving it out, but you can substitute honey if needed, but reduce the honey to 1/2 cup (170g).
I love this recipe. My young daughter and I both enjoy a sweet snack but these are a nice way to get that sweet fix with the added fruit benefit. The recipe is really robust and forgiving, I’ve made batched where I’ve subbed the fruit for what I have (pears, pumpkin) and they’ve still turned out delicious.
These were so good. Sometimes “healthier” muffins turn out dry or rubbery, but not these. So soft and flavorful. Thanks for this great recipe!
I didn’t have coconut oil, so I swapped about 1/2 cup of wheat flour with 1/2 cup coconut flour, and the end result still had that hint of coconut flavor. Plus coconut flour adds additional fiber, which is always a plus in my book.
Because the coconut flour absorbed more liquid than wheat flour, I added an additional 2 tbsp of milk to make the batter less thick. It came out great!
Hello! My son cannot have dairy or egg so this recipe looks delicious! These are the two substitutes I like to use, which would you recommend? either 1/4 c of applesauce per egg or
a combination of one teaspoon each of baking soda and white vinegar to replace one egg.
Hi Lenna, We wish we could help but we haven’t tested this recipe with any egg substitutes. Let us know which one you try!
Easy to follow, and what a success!!! Can’t wait to try your other recipes ❤️