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 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.
Can I add oatmeal to this recipe?
Hi! You could certainly try adding some oats. We haven’t tested it but we would start by replacing 1/3 cup of flour with 1/3 cup of oats. Let us know if you give it a try!
First off thank you Sally for your delicious recipes! I started baking during Covid and I am a huge fan of your website! I have made this apple muffins recipe using small chopped apples from our golf course and homemade apple sauce from the same apples.
I would like to make another batch as I still have leftover apples and to thank the staff at the golf course. My question is I want to make them without the nuts because of nut allergy and make them a little bit sweeter because the apples are tart. Should I increase the amount of apples and the amount of honey? How much? and can I put chocolate chips?
Hi Tanya, thank you so much for the kind note and feedback! You can certainly omit the pecans OR swap them for chocolate chips as you mention. We don’t recommend increasing the amount of honey as that will add more liquid to the batter and they may not bake up correctly — likewise with the apples. How about adding some coarse sugar on top before baking for a sweet and crunchy kick?
Absolutely delicious!! So simple too. Thanks Sally. Shared this recipe with those I know!
Sally, your recipes stand the test of time, looking back when this recipe was first published and you are still getting comments! Thank you for your work to bring your readers such well-tested recipes.
I made these tonight because I wanted something a little more healthy for my visiting 10 year old grandson. My only substitution was using 1 cup applesauce as I did not have any apples. I threw in 1/4c homemade yogurt that wouldn’t fit in the jar. Mine did not bake as high or pretty as yours but I didn’t expect it with no shredded apples. They tasted delicious, and I did not taste the maple syrup as overpowering at all. Used Penzy’s Pie Spice, which gives them a more complex spice flavor I think. Nice to have a little warm spice in August:)
We’re thrilled you enjoyed these muffins, Cindy! Thank you so much for making and trusting our recipes 🙂
These are delicious, Sally!
Any advice for reheating a batch for a brunch? I made them a day ahead. Thanks!
Hi Kennedy! You can cover the muffins in foil and bake at 350 for 5-10 minutes, then check to see if they’re warm. The trick is warming them without drying them out – let us know what you try!
I made these muffins last week and they are really delicious!
As much as I love the butter-and-sugar world of baking, I try to mix it up with healthier options sometimes.
What I love about these and the whole wheat banana nut muffins (thank you for that recipe too) is that, while it’s a lighter version of the traditional muffin, the flavour hasn’t been sacrificed.
Thanks a bunch for these awesome recipes!
Hey Sally! FIrst things first (I promise I have a question but I have to say this first) OMG thank you for helping me discover my sincere LOVE of baking. Like I literally just sold all my stuff so I can go to baking school thanks to this blog. Your recipes put to paper the ideas I have, and I’ve been able to learn better food science because of your detailed posts. This has been a huge win for me during an uncertain time, after 10 years of trying to find my passion. So… YOU GO GIRL!!!!
I’ve been playing with your master muffin recipe and am excited to try this healthier one now (due to the many jumbo full fat muffins I’ve consumed in the last 4 months).
Just wondering if I could substitute in some oats… say 1/3 of the flour swapped? I was also curious, most of your other muffin recipes call for sour cream or yogurt. Is the reason it was omitted from this recipe because the maple syrup is more moist than the granulated sugar? I am considering doing the recipe above but doing half maple syrup, half brown sugar, so curious if I should add maybe… 1/4 cup of yogurt?
Thanks!
Hi Abbey! I’m just seeing this wonderful comment and question now! Thank you for your incredible kindness. It’s so nice to hear from you and I’m so happy to read that my recipes have inspired you in such a profound way! Best of luck to you on this new chapter. 🙂
Regarding this muffin recipe, you could certainly add some oats. I think if you’re making the other changes (half maple syrup, half brown sugar) that you could replace 1/3 cup of flour with 1/3 cup of oats. Add some yogurt or sour cream since you’re reducing the maple syrup. Even 1/4 cup could help. I’m interested to hear how they turn out!
Good evening! I would love to make these a head of time, for a gathering. Could I freeze these? They look awesome
Hi Sarah, absolutely! For longer storage, freeze muffins for up to 3 months. Allow to thaw overnight in the refrigerator, then bring to room temperature or warm up in the microwave if desired.
Made these today with grapeseed oil (instead of coconut), honey (instead of maple), homemade applesauce instead of grated apple (quicker) and added 3/4 cup/75g whole oats otherwise I followed the recipe exactly. My add ins were hemp seeds, chopped and toasted walnuts and an apple chopped (to use up old apples). Light, fluffy and moist wholemeal muffins, so so good! The hot air trick is genius, thank you for the recipe.
Absolutely delicious!! The BEST apple cinnamon muffins recipe ever!!! I love the fact that they are healthy and sooo fresh and moist and yummy. Thank you so much!!
Would these work with peaches, canned or frozen? I’ve made them as is several times, love the recipe. Would like to keep the base and switch things up.
Hi Christine, that should work fine, just be sure to drain and blot any extra moisture from the peaches as they’ll add more liquid to the batter than the apples. Or, you might like our Peach Streusel Muffins as well!
I normally love your recipes, so I don’t make any changes. But this one was way too dry. I didn’t care for the flavor either – the whole wheat flour outpunched the apples and cinnamon, which was a bummer. I would make these with AP flour in the future.
Thank you for the delicious recipe, Sally! I made this recipe today and the muffins turned out amazing. The only add on was 1/4 cup of brown sugar, since I did not have enough maple syrup.
OMG, I just made these and they came out so amazing! The only modifications I made was using only 1/3 cup maple syrup and using olive oil. I’m so impressed with how great they came out. Thank you!
These muffins are great. Just made them the second time, first time they were perfect and moist, second time they were drier. Second time I couldn’t grate the apple though (had to chop) and used coconut oil instead of canola, plus I’m using an oven that seems to cook hotter. On this second time though I made maple glaze from your maple scone recipe. Used Grade B syrup and subbed maple sugar for 1/4 of the powdered sugar then dunked these puppies in. It’s absolutely dreamy. The remaining maple glaze is going to get drizzled over the Guinness frosting on your Guinness brownies in two weeks!
I followed the recipe exactly and these are soo delicious! Almost too delicious! How can stop after just one lol! Can’t wait to browse some of your other recipes 🙂
Looking forward to trying these! What can I replace the applesauce with? Can I use plain greek yogurt and how much? Thank you
Hi Kim, Greek yogurt (same amount) would work, or you can use an additional 1/3 of oil. Hope you enjoy them!
Great muffins. I made them exactly as directed and they came out perfect. The allspice is the magic ingredient! Everyone commented on how good they smelled before they even took a bite.
Thank you for the recipe!
This is one of the best muffin recipes I’ve tried with all whole-grain flour (and I’ve tried a lot of them). Very light in texture, full of flavor, and thoroughly satisfying!
My favorite go to muffin recipe!
Sally God bless you! These were the best cinnamon apple muffins I’ve ever tried! I didn’t have pecans so I omitted that, and used coconut oil…so delicious. Thank you for sharing this wonderful recipe!
I tried this recipe today, halving all ingredients. I replaced the applesauce with Greek yogurt and added chocolate and peanut butter chips. The result came out beautifully! The muffin is still moist and soft, and delicious! Thank you for this recipe Sally.
I made these 2 days ago and they were great. I only had wholemeal flour but I decided to go totally rogue and hand grind some whole wheat course grain bulgur (about 3/4 cup) and 1/2 cup LSA meal mix instead of the full 2 cups flour. I added crushed walnuts as well as I didn’t have quite enough pecans. I also randomly added 2 table spoons of puffed amaranth. I didn’t have the applesauce so I used the 2/3 cup coconut oil as recommended. Otherwise I followed the recipe exactly. These muffins are so good. They have an incredibly healthy taste and that whole grain savouriness I was craving! My chef partner admired them although wanted them sweeter, but for me they are perfect. My only change next time would be to make an apple sauce because the coconut oil flavour was a little dominant over the apple. Ps the tip about starting at high temp worked really well.
I just made these and there amazing! I only used 1 apple and replaced the oil with olive oil and the apple sauce with yogurt. Definitely recommend these especially for a cold day since these feel so cozy 🙂
Sally, these are delicious! The only thing I did differently was to exchange the whole wheat flour with half white whole wheat and half AP.
I have tried several of your recipes, and found most delicious! Thank you for sharing!
Cant wait for my kids to have these for breakfast. They look and smell delicious
Made these yesterday, and they were pretty good! I made a few substitutions based on the ingredients I had; I replaced 1/3 cup of the maple syrup with 1/3 cup coconut sugar, used all-purpose flour instead of whole wheat (simply because I didn’t have it in my pantry, though I hope to use it next time), and replaced the applesauce with an equal amount of melted butter. As I said, they were pretty delicious, but there are a few changes I want to make next time: (1), the apple flavor wasn’t as pronounced as I would like, probably because I omitted the applesauce, so I plan to add apple chunks in along with the grated apple. (2), a little less cinnamon; I found that 2 teaspoons overpowered the apple, and while I love cinnamon, I still want to taste the apple, so next time I’ll reduce it to 1 1/2 teaspoons. Aside from that, they looked and tasted great, and they smelled AMAZING while baking; I had them in the oven while preparing stew for dinner, and got to inhale the tantalizing aroma the entire time 🙂 Someone ought to take the scents of baked goods as they’re baking and bottle it; I’d wear a perfume like that any day!
I added fresh chopped cranberries, a pinch of nutmeg, and cloves. Sprinkled coconut sugar on top before baking. Pretty freaking fantastic. Thanks!
I had some past-their-prime apples to use up and searched the web for an apple-based, whole wheat muffin and saw a link to this recipe. Thanks so much for sharing it – it’s absolutely delicious, and will be a regular treat in our household.
It turned out really well even though I made a few substitutions: 1:1 homemade date paste for maple syrup; instead of 3 eggs, 2 eggs plus 1/8 cup liquid egg white; and more each of applesauce (100-gram single-serving containers were all my grocery store had – pandemic shopping!) and apple (I used two whole honeycrisp apples for a total of 382 grams of shredded apple). I figured the extra liquid from apples and applesauce would compensate for the thickness of the date paste, and wasn’t too far off; I baked them for an extra 9 minutes, and will probably bake the next batch for a further 5 beyond that.
The extra apple and applesauce meant more batter, so I made 19 instead of 15 muffins.
Thanks again!
I loved the shape and texture of these muffins, the only thing that I disliked a bit was the overwhelming maple taste. I like maple, but this was a bit much for me. However, it may have been that we used strong, dark maple syrup, which has a lot of maple taste. I think next time I would do just 1/3 cup maple syrup to reduce the sweetness and maple flavour. Also, I used 1 egg and 2 flax eggs, which worked really well. I’m trying to cut down on using actual eggs for baking since we’d have to shop all the time if we used a ton of eggs.