Healthy Apple Muffins
Amazing, healthy apple muffins made with maple syrup and whole wheat flour! No one will guess that this simple cinnamon apple muffin recipe is healthy, too.
Updated by Kathryne Taylor on August 30, 2024
When you buy through our links, we may earn a commission. Learn more
It’s apple muffin time! You all really seem to love my banana muffins, pumpkin muffins and carrot muffins and the blueberry muffins in my cookbook. Today, apple muffins are joining the club.
Like the others in the bunch, these muffins are made with 100 percent whole wheat flour and naturally sweetened with maple syrup or honey. They are nice and fluffy, with just enough sweetness to be irresistible.
Granted, I already have an apple oatmeal muffin recipe on the blog from four years ago, but I have significantly upped my muffin game since then. These muffins are the better of the two, by a long shot.
I based these healthy apple muffins off my carrot muffins, replacing grated carrots with fresh apple, and replacing half of the Greek yogurt with applesauce.
These muffins contain apple, three ways: freshly grated and chopped apple for the perfect texture, and applesauce for infused apple flavor. They’re the best apple muffins I’ve ever had.
Healthy Apple Muffin Notes
- These apple muffins taste even better after resting for a few hours, if they last that long.
- I particularly enjoy them with a spread of peanut butter.
- Check my recipe notes for how to use honey instead of maple syrup, and some ideas for how to make the muffins vegan.
I think it’s time for another! Please let me know how you like these muffins in the comments. I love hearing from you.
Baking Tips for Success
How to Measure Flour
How you measure your flour is important. Why? If you measure incorrectly, you could end up with up to 50 percent extra flour, which will make your muffins dense, dry and flavorless. Use the spoon and swoop method:
- Gently stir your flour to loosen any clumps.
- Spoon your flour into the measuring cup with a big spoon or a flour scoop. Do not scoop up the flour directly into the measuring cup.
- Level off the top of the cup with a knife. Repeat as necessary.
Baking Powder & Baking Soda Are Not the Same Thing
…and they are not interchangeable. Both are leaveners that help your baked goods rise (baking powder contains some baking soda, but that’s a long story).
This recipe relies on a combination of baking powder and baking soda to produce light and fluffy muffins. For ideal results, always follow the recipe and measure carefully.
How to Stir Your Batter
This muffin batter is super simple to stir together by hand, and that’s how I recommend making these muffins. Why? Whipping your batter will make the flour’s gluten protein too strong, yielding tough muffins.
I know it can be tempting to use a stand mixer or hand mixer when it’s within reach. Please don’t! Follow the instructions below and you’ll end up with light, fluffy muffins.
Watch How to Make Apple Muffins
Healthy Apple Muffins
Amazing, healthy apple muffins made with maple syrup and whole wheat flour! No one will guess that this simple cinnamon apple muffin recipe is good for you, too. Recipe yields 12 muffins.
Ingredients
- 1 ¾ cups white whole wheat flour or regular whole wheat flour
- 1 ½ teaspoons baking powder
- 1 teaspoon ground cinnamon
- ½ teaspoon baking soda
- ½ teaspoon salt
- 1 cup grated apple
- 1 cup apple diced into ¼” cubes
- ⅓ cup melted coconut oil or extra-virgin olive oil
- ½ cup maple syrup or honey*
- 2 eggs, preferably at room temperature
- ½ cup plain Greek yogurt (I used full-fat but any variety should do)
- ½ cup applesauce
- 1 teaspoon vanilla extract
- 1 tablespoon turbinado sugar (also called raw sugar), for sprinkling on top
Instructions
- Preheat oven to 425 degrees Fahrenheit. If necessary, grease all 12 cups on your muffin tin with butter or non-stick cooking spray (my pan is non-stick and doesn’t require any grease).
- In a large mixing bowl, combine the flour, baking powder, cinnamon, baking soda and salt. Blend well with a whisk. Add the grated apple (if it is dripping wet, gently squeeze it over the sink to release some extra moisture) and chopped apple. Stir to combine.
- In a medium mixing bowl, combine the oil and maple syrup and beat together with a whisk. Add the eggs and beat well, then add the yogurt, applesauce and vanilla and mix well. (If the coconut oil solidifies in contact with cold ingredients, gently warm the mixture in the microwave in 30 second bursts.)
- Pour the wet ingredients into the dry and mix with a big spoon, just until combined (a few lumps are ok). The batter will be thick, but don’t worry! Divide the batter evenly between the 12 muffin cups. Sprinkle the tops of the muffins with turbinado sugar. Bake muffins for 13 to 16 minutes, or until the muffins are golden on top and a toothpick inserted into a muffin comes out clean.
- Place the muffin tin on a cooling rack to cool. If you have leftover muffins, store them, covered, at room temperature for up to 2 days, or in the refrigerator for up to 4 days. Freeze leftover muffins for up to 3 months.
Notes
Recipe adapted from my healthy carrot muffins.
*If you are baking with honey: Honey tends to brown quickly, so to avoid overdone muffins, bake muffins at 325 degrees Fahrenheit until a toothpick inserted in the center comes out clean, about 23 to 25 minutes.
Make it vegan: Replace the eggs with flax eggs and replace the yogurt with vegan buttermilk—try mixing 1 ½ teaspoons vinegar with a scant ½ cup non-dairy milk. Let it rest for 5 minutes before adding it to the other liquid ingredients. (You could also try using more applesauce in place of the yogurt but I’m not sure it’s acidic enough to counteract the bitter taste of the baking soda.)
Make it dairy free: See “buttermilk” option above.
Make it egg free: Use flax eggs instead of regular eggs.
Make it gluten free: Bob’s Red Mill or King Arthur Flour make gluten-free all-purpose blends that work well.
Nutrition
The information shown is an estimate provided by an online nutrition calculator. It should not be considered a substitute for a professional nutritionist’s advice. See our full nutrition disclosure here.
Hi . These sound great ! Do you know what color they would be on NOOM ?
I’m not familiar, sorry!
Can we use regular yogurt instead of Greek yogurt. Thanks
Loved them. I substituted flour with Robin Hood Gluten Free flour. They were delicious only thing I would do differently is add more cinnamon. Made these because my son is gluten sensitive, have had terrible luck with gluten free recipes but these were very good.
Hi Kate!
I’ve tried a few of your recipes and love them. Gonna try this apple muffin next. Could i substitute all the whole wheat flour with oat flour? If yes, how much should i use? Thanks!
Hi Anne! I haven’t tried oat flour with these. I would be interested to see how it would work, but it should if you follow my how to oat flour tips. It is more delicate so the weight of the apples may be tricky. Be sure to increase the volume of the oat flour, per the post, to ensure you have enough. It’s all laid out in the How to Substitute Oat Flour. Let me know how it goes for you!
Hi Kate!
I followed your substitution tips and used 2.5 cups oat flour and the muffins turned out great too! I made the apple sauce with your recipe as well. Delicious! Thanks for the tips :)
I tried this recipe today and loved them. But I used paper muffin liners and the paper stuck to the muffin. I guess for this recipe its best to just grease the pan?
Did they stick still after they had cooled completely? I always use paper cases, I find they stick when warm but you can peel both Em off once cool!
I make these all the time now, a big hit in my household!
Awesome recipe! First time making these today- turned out delicious! No surprise here! I’ve made your pumpkin, blueberry and banana muffins before and they’re all great – this healthy apple one might be my favorite though. I love how versatile it is and the notes you share. I didn’t have yoghurt, so I used flax milk and vinegar. I was too lazy to make applesauce so I mushed up a large banana instead. They turned out moist and fluffy!
I’m glad you loved these! I do love muffins, so I’m glad you have tried so many. I appreciate your feedback and review, Eva.
I love this recipe! Though my husband is allergic to yogurt. Can I substitute it with anything? He would love these! Thank you!
Hi Melissa! See the vegan notes below the recipe instructions on an alternative. I hope you can enjoy them!
I made these recently and they were amazing! I love all of your recipes, and I especially love that these muffins aren’t overly sweet. The apple flavor shines and they were actually filling enough to count as a solid breakfast!
Another muffin recipe! Look at you go, Oksana. Thank you for taking the time to review!
How do you think it would go if I substituted cooked rhubarb for the applesauce? I haven’t made any of your recipes before, but keen to give this one a go – and have plenty of rhubarb to cook, but not many apples to do the appplesauce :(
Hi Nicki! I haven’t tried rhubarb and apple together, but if that sounds appealing to you flavor-wise, I think it would work!
I di exactly that, and they taste amazing!
I decided NOT to SQUEEZE OUT some of the liquid from the GRATED APPLE in the recipe for Healthy Apple Muffins, AND I ADDED 3/4 CUP OF SULTANA RAISINS, in the “single” recipe, to soak up the liquid from the grated apple if there’s too much of the liquid in the muffin batter … and it turned out to be perfect. And in the “double” recipe, I added 1 1/2 cups of Sultana raisins, and for the “triple” recipe, I added 2 1/4 cups of Sultana raisins. I don’t like to throw away any nutritious part of an ingredient … an “apple liquid” is APPLE JUICE which is FULL OF MINERALS, and vitamins, etc. So, why discard it? Just soak it all up with some Sultana raisins which will PLUMP UP NICELY in the Healthy Apple Muffins.
Best muffins I ever made. It’s a hit with everyone one in the family
Leena
Perfect! I followed all directions using granny smith apples with the addition of a cup of chopped walnuts and 3/4 cup dried cranberries. Cooking at 425 for 15 minutes, they were still not done so I decreased to 325 and cooked 5 more minutes. So good!
I followed the recipe exactly and they were SO GOOD! My whole family gobbled them up in a day. Making another batch today!
Hi!
Am I able to use unbleached all-purpose flour instead of whole wheat?
Yes, that will work well!
This Recipe is AMAZING!! I made them today and they’re almost gone. I used Pink Lady Apples and they turned out great, Thank you for this recipe. I’ll make sure to share it!
I’ve just discovered your recipes and I am going to try the banana muffins tonight.
The ingredients and method are so clear and I’m hoping for a great result. I will let you know the result
Hi Kate
Just wondering whether I’d be able to use almond meal/flour in replace of regular flour?
Thanks
Bec
Hi Rebecca! I don’t recommend almond flour as a good 1:1 substitute. If you need it to be gluten free, try a gluten free all purpose flour or check out my oat flour post. Oat flour could work here.
These seriously are the best muffins I have eaten! So moist, tons of apple flavour, and I love the fact that I can use honey instead of sugar. The Greek yogurt, and coconut oil come through so well and bring a great flavour. These will become my go to recipe for sure!
Awesome!!! I didn’t have Maple Syrup and was saving the honey for another thing, and because I’m from PA Dutch extraction and we use a lot of it, I used Molasses! Everyone (Wife and Growed-Up Daughter) loved them. So moist and the texture was great!
This was the worst muffin recipe ever……NOT!!!!!! As I fooled my 6 yr old by saying, “Do not eat these muffins. They are terrible. They are especially bad warm with butter.” LOL
I didn’t have yogurt so I made buttermilk with 1.5 tsps lemon juice and scant 1/2 cup milk. Also….mommy brain…when I put the muffins in I accidentally changed the oven temp to 170 degrees because I thought I pushed “timer”. I have no idea how long I cooked them but they came out perfect at an unknown time and unknown temp. LOL
So basically….these seem like foolproof muffins.
So good!
First time I made these muffins, they were so wonderful I’d love to replace the olive oil for a little one that can’t have much fat in her diet. I thought I read somewhere that you recommend replacing with extra applesauce but when looking again to confirm and how much, I couldn’t find info
I’d love some direction
Thank you
Hi Nancy! I’m happy you loved them. I personally haven’t replaced the oil with applesauce, but do know that it can work in some applications. Typically the same amount, but can’t be sure without testing it. I know others have tried it in some of my muffin recipes. If you try it, let me know!
I certainly will
Thank you for such a quick response
Hi, can anybody suggest a replacement for the apple sauce – if it’s the only ingredient one is missing and too lazy to go to the store …
sub an overripe banana for the apple sauce any time!
I’ve taken the healthy apple muffin recipe, which was terrific as is and replaced the oil with same amount of applesauce due to a little one who medically cannot have much fat in her diet I treated the extra applesauce the same as if olive oil and proceeded to bake you end up using (unsweetened applesauce in my case) twice in the recipe They taste wonderful and the consistency is moist as was with the oil
Baked for 19 min
Yummy
Thank you for sharing and I’m happy it was able to work with what you needed!
My favorite muffins. Like she said- hard to believe they are so healthy!
I have made these twice now. And they are amazing! I made them with honeycrisp apples the first time and then with green apples the second. Simple and delicious! Thanks for another great recipe!
Love the muffins.love all your recipies.
Can I use self raising flour and just omit the baking powder
Haven’t got the Greek yogurt – anyone tried Vanilla favoured yogurt??
Hi John! That may be a little too sweet with the other ingredients, but let me know if you try it!
Hi, if I don’t have applesauce what can I substitute it with or can I just leave it out?
Hi Jess, unfortunately you don’t want to omit as baking is quite precise. Sorry!
Very sorry but I’m afraid this didn’t work for me, although i will say i’m not a great cake baker. Muffins were extremely ‘wet’ and not sure why had to have grated, chopped and purreed apples, rather laborious given the finish.
I made these for my baby as mini muffins, so I omitted the maple syrup to reduce the sugar content. And I didn’t have applesauce so I just used grated apple instead (and used more grated instead of chopped to avoid chunks). They turned out great! Very moist and still delicious without the maple syrup :) Baby and I both approve! I love that I can give him a delicious muffin as a snack and know that it is full of good ingredients, fruit and protein.
We love this recipe and have done it many times. My kids really like the Apple and spices.
Would it work as a loaf?
Hi Julie! I haven’t tried it as a loaf. You could try it, just be mindful of baking time as it will likely need more.
I made it today and added 2 grated carrots, 1mashed banana, a good handful of currants, a handful of oats, nearly a cup of almond flour and 1 cup of flour.
I used half the maple syrup because thats all I had. Oh and I forgot to add the bicarb with the rest of the ingredients. Topped the loaves with raw sugar for some crunch. I had a fair bit of mixture so I put it into 2 loaf pans and baked at 180c for 50mins to 60mins. Looks like you can fiddle with this recipe quite a bit as this was one of the nicest fruit loaf I have made. I also added in a cup of chopped walnuts. Very yummy..hubby and son thought so too.
These were light and fluffy, but could have used more flavor. Next time I’ll double the amount of apple for sure!
Yum!
Would it be possible to substitute greek yoghurt with sour cream?
Hi Sasha, sorry for my delay! I think that could work, but I haven’t tried it. Let me know how it turns out for you.
I made these today using sour cream in place of the greek yogurt and they are yummy!
Hi Kate! I saw you have a previous recipe that includes oats. If I wanted to add oats to this recipe instead, any advice on what else I should change?
Thank you.
Hi! You should be able to add oats to this recipe. Follow my strawberry oats muffin for recommendation.
Awesome, thank you! I’ll definitely look into your recommendation.
Wow thank you for such a detailed recipe. I was really impressed with how the recipe and additional information was laid out. In particular, loved how you commented on how the batter should turn out (I’m always wondering this when trying new recipes!). I used the pulp from pressing apple juice instead of the shredded and added a bit of cloves. Delicious! Thank you!
You’re welcome! I’m glad you loved the detail and that it worked out well.
Could you not just use grams for measuring? Then there would be no confusion with measuring flour.
Hi Charli, sorry for your frustration. Since the U.S. has different measurements, that’s my standard.
Hi Kate,
Yes, I agree with Charli- it would be helpful to have the apple chunks, grated apple, and flour measurements given in ounces or grams to avoid confusion. Thank you. I’m going to make this today because I have a lot of leftover apples that are getting soft.
I think I will try this for baby’s first birthday. Do you think your medjool date cream cheese frosting would work with this recipe for a more ‘cupcake’ look?
Hi David, Happy birthday to the little one! Yes, I think that is a great idea. I hope it’s a hit!
A hit indeed! We can’t stop eating them!! Thanks for the great recipes and ideas!
These muffins are the family fave!!! With it being apple season, we have experimented with several different varieties (right from the farmer!) and the muffins are great every time. For a back to school treat, I hid a caramel square (I froze it first) half way down – definitely a hit. Just made some today with cheese half way down and some on top….still too hot to try but they look great.
I usually love all your recipes!!! Big fan!!! However, in this one, the coconut oil really stood out. I wonder where I went wrong!! Maybe it’s cause I used red apple? (McIntosh)
I’m sorry to hear that! The apple flavor can impact things, but it shouldn’t that much. Are you sure you got the melted quantity?
AMAZING FLAVOR! Made the yesterday and making again today!
I have a load of homemade apple sauce that I want to use up, could I use that in this recipe or would it be too wet? Thanks
Hi Elizabeth!For this recipe, you will only want 1/2 cup, per the instructions.
Does it matter what type of apples you use? Can I use gala? Thanks in advance.
I prefer the ones in this recipe, but you can use the apple you prefer! Let me know what you think.
Do you think sour cream is a good substitution for the greek yogurt? Hoping to try this recipe in the am.
All your recipes I’ve ever made have been fantastic!
Hi Alex! It could work, but I haven’t tried it. The yogurt does have a little more moisture do your results may be impacted some.
Hi Kate! I live your recipes! They are easy, healthy and full of flavor! These are the best apple muffins. I used gala apples, put walnuts in the batter, added 1 tbsp brown sugar, and added 1tbs butter as well. I only have low-fat Greek yogurt and I felt like they were a little dry. I make these regularly during fall and winter. Great with a cup of tea!
These muffins turned out wonderfully! I thought I would share some of my substitutions. 1. Used mashed banana instead of applesauce 2. Sour cream instead of yogurt 3. Honey crisp apples. The muffins were moist and delicious. Thank you Kate as always!
Thank you for sharing, Suzanne! I’m happy to hear you had such great results.
Wow! These were really light, flavoursome and moist muffins!! Brilliant way to use up those fall apples. I used honey instead of maple syrup – and used less than 1/3 cup, instead of 1/2 cup. I also subbed some of the apple sauce with mashed banana.
Delicious!
Thanks for the healthy apple muffin recipe! The texture was great. I used homemade applesauce and apples from our local orchard, and yet, I still felt like these could have been more flavorful! I don’t know if I maybe squeezed too much of the apple juice out of the apples?! Followed the recipe to a tea. Love the ingredient list, and they came out beautifully. May add more cinnamon next time??
Hi Amanda! I’m sorry you didn’t think these were as flavorful as you were hoping. What variety of apples did you use? You can add more cinnamon if you like. I appreciate the feedback!
Hi! Does this use pure maple syrup, or the Aunt Jemima sort of maple syrup?
Hi Anna! I like pure maple syrup.
Good reminder regarding voter registration. But don’t take the link as gospel . . . It has an error on my state. There is early voting in SC and it starts October 5.
Good muffins. :)