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.
Did quite a lot of baking today! Made these apple muffins (which I’ve had before and adored), and the blueberry muffins (which are in the oven as I’m typing this) in loaf pans; I’ll leave a comment for the blueberry muffins on that recipe. For my apple loaf, I made it vegan by using flax eggs and Anita’s Organic Coconut Yogurt (which is the best and least processed of all non-dairy yogurts, in my opinion, that are store-bought). Additionally, I used a heaping teaspoon of cinnamon, heaping 1/4 tsps. of cardamom, ginger, and cloves for added spice. I didn’t have Granny Smiths, so I used two huge Honeycrisps (I didn’t measure them out). I used organic, unrefined, cold-pressed coconut oil and organic maple syrup, and used organic erythritol in place of the turbinado sugar topping. I plan on letting the loaf cool, then putting it in the freezer and having it for breakfast over the next few weeks! Thank you for such an amazing recipe, Kate!
Thank you, Alex!
Wow, are you my soul sister? Lol! I bake with ginger and cinnamon— no matter what I’m making. Orange muffins? Yup! Banana bread? It’s there. Your creations sound delish. Enjoy your day!
A Southern California Mom
Hi, could you please let me know what size loaf pan you used and how long you baked it for? I’d love to try this as a loaf/bread
I really want to add carrot to these apple muffins. Do you know how I could do that? Or add apples to your carrot muffins?
I made these and they were so good! My son begged me to make more. I did not have two apples but grated in a carrot and ran low on cinnamon so used pumpkin pie spice. It’s a really forgiving recipe, so easy to experiment with it a bit.
I like the carrot idea! Seems like it would be a good mix that would make it tasty & healthy :) Looking forward to your response to this Kate!
I just made your recipe and I love it! Thanks for a delicious healthy muffin!
You’re welcome, Miranda! I’m happy to hear that.
I’d love to add oats to this recipe for some added fiber, how would you adjust the recipe? Love the muffins; they were delicious!
Hi Laura! You should be ok to add 1/3 cup rolled oats without any adjustments. Let me know what you think!
Can you substitute the whole wheat flour for oat flour?
Unfortunately, I don’t think oat flour will work as a 1:1 substitute. If you try it, let me know!
This is my favorite so far didn’t add the sugar on top because to me it was not needed it was perfect level of sweetness as is
Thank you for a really great recipe
You’re welcome, Debbie!
Wow I found this recipe by accident and boy it is a keeper. Huge hit with the husband and l, we loved them. So light and flavorful so next time I will make a double or triple batch and freeze. I will definitely be trying more of your recipes.
I’m happy you came across this recipe, Alison! Thanks for the review.
I made these muffins mainly because I had all the ingredients and needed an easy dessert. My guests LOVED the muffins and asked to take a couple home with them. They are yummy for breakfast with coffee, but with the sugar on top, they are a great dessert too. I didn’t change anything in the recipe, but they did make 18 muffins instead of 12.
Thank you, Janet!
These taste great! I added half a cup of chopped walnuts.
I was afraid the batter would overflow my muffin tins (as it turns out they don’t rise so much) so had a good bit of batter left and baked it in a standard loaf pan, and that loaf turned out to be about an inch plus high. All of it was delicious, and I think next time I’ll just make a loaf rather than muffins. Do you think that would work, and what would you suggest for the time and temperature?
I was wondering too if there’s something I could use for applesauce. I don’t keep applesauce around, so made my own just for this because I didn’t want anything to go wrong. Why not just more grated apples?
Hi thank you for sharing!! I was curious if I would be able to substitute the flour for almond or coconut flour and how much would I use? I’m trying to keep my carbs really low. I cant wait til taste them. :-)
Hi Mickey, I think you might love my apple and carrot muffin recipe, which calls for almond flour. You can simply replace the shredded carrots with more grated apple if you want apple muffins!
I used purees bananas in place of apple sauce and they turned out wonderful!
Could coconut flour be used to help with the carbs? If I wanted to add a little more fiber could I use psyllium husk powder or flaxseed meal?
Hi Ashley, I don’t recommend using coconut flour. It hasn’t worked well for me in the past and provide the same result. You have to change the recipe a lot to suite the needs.
Hi This looks like a great recipe. Would it be possible to make it lower sodium?
You could limit the salt, if you need to.
Hi Kate
Love these muffins! I’ve modified them a bit so I could lower the pts since I am following Weight watchers. Instead of 1\2 cup of maple syrup I use 1\3 and instead of 1\2 of oil I use 1\4 cup of olive oil. I also use one grated apple and one chopped apple. I didn’t intend to do this just misread the recipe but it turns out really good. I cooked them in my mini-muffin tin and they equal 1pt per serving. Which is fantastic. I can have a little sweet snack without any guilt! Can even have two!
Thanks for sharing, Francine!
I found that they could be a little bit sweeter, possibly adding an extra 1/4 cup of maple syrup would really help!
Thanks for your feedback, Autumn!
I think this recipe is great! I added the 1/3 cup of oats with no alterations to the recipe as you suggested in a reply to another comment and the muffins are delicious with a great moist texture.
I used honey with the adjusted temp. and time and that worked out perfect too.
I had coconut sugar in the cabinet for sprinkling on top and that was a success as well.
Thanks for the great recipe!
Thank you for sharing, Erin!
My sometimes fussy teen thought these were very yummy! Thanks for sharing this recipe. :)
You’re welcome, Shannon!
Cry for help: Unrefined coconut oil has a smoking point of 350 degrees F, but you advise baking these muffins at 425 degrees F. Maybe you meant that we should preheat the oven to 425 degrees F and then, after five minutes, decrease the heat to 350, but your cooking time does not reflect this for anything save the use of honey rather than maple syrup. I prefer honey to maple syrup and used syrup in the past when I made your muffins successfully but fear that reducing the heat to accommodate the coconut oil’s smoking point of 350 might not be good for these muffins if I continue to use maple syrup, not honey.
As indicated, I made these muffins several months ago (with pears and apples), and they were great, so maybe the unrefined coconut oil was not the problem when I made these again yesterday. Maybe I heated the oil on my cooktop to liquefy it too long, part of the time at a higher heat than necessary, or didn’t cool it thereafter for five minutes before moving on to Step 3 in your recipe. Maybe my Granny Smith apples had gone bad; they looked all right, but I’d had them for quite some time. Maybe the Bak-Klene ZT Baking Spray that I used to grease my conventional muffin tins had gone bad over time in my dark pantry.
So many variables here, but I hesitate to make these muffins again until an experienced baker like you provides advice. I’d hate to replace my coconut oil, my cooking spray, and my apples and vary cooktop and oven times absent your counsel. Heck, I’d hate to toss the 16 muffins I made yesterday, sacrificing labor and expensive ingredients.
Extra-virgin olive oil typically smells herbal. Do you really ever sub this for coconut oil?
Sadly, the rancid taste of my second-time-around Healthy Apple Muffins remained even after these muffins had cooled almost completely on wire racks, and the one I ate this morning, taken from a plastic bag in our fridge, was just as disappointing despite my use of the turbinado sugar as a topping and the sweet, fresh jam I used on each half.
My rating reflects my problem with your recipe or my ingredients and/or carelessness
Suggestions?
Hi Marj, I’m so disappointed that the muffins didn’t turn out well for you! The coconut oil should be warmed just to the point that it’s melted, and then you can measure it and mix it properly. I frequently use coconut oil (unrefined) in baked goods at this temperature and I have never had an issue with the smoking point. That’s more likely with, say, roasted vegetables.
If your muffins tasted rancid, I suspect it was due to either your apples being bad, or quite possibly your whole wheat flour has gone bad. Whole wheat flour doesn’t have as long of a shelf life as all-purpose, since it contains the naturally-occurring oils found in wheat berries. If your whole wheat flour smells off, it would definitely make your muffins taste bad.
And yes, I have used extra-virgin olive oil in muffins based on this recipe and they turn out great. I would recommend using a mildly flavored olive oil, such as California Olive Ranch Everyday. Hope this answer offers some insight!
Hi! I really want to try this recipe, but I’m following noom and need the amount of calories. Is it possible to get that? Thanks!
Hi Brittany! The nutritional information is below the notes of the recipe. You just need to click to expand and make sure you allow cookies as this is a plug-in on my site.
Made these muffins last week and my husband said these were the best apple muffins he has ever had! Currently popping another one in the oven now, making it into a bread instead of muffins this time, so hoping not will still cook correctly!
That’s great to hear, Maria! Thanks so much for sharing.
This is a great recipe!! I had a bunch of apples left from last year’s harvest & I was determined to use them all. Instead of using applesauce & grated apples, I just finely diced up ALL of the apples & threw them in. I put in a cup of yogurt & increased the cinnamon 4 fold. I wasn’t sure they would turn out with my deviations but they did. They are unbelievably good!! My husband likes them too. Thank you for creating & sharing this recipe
I’m glad they turned out, too! Thanks for the comment Deanna.
Flavor was good, but something is wrong with the recipe. There was way too many liquid ingredients for the amount of flour. I had to keep adding more flour and ended up with 20 muffins!
Hi Lois, that shouldn’t be the case. I’m sorry this didn’t turn out perfectly for you. Are you sure you didn’t measure too much liquid/ not enough flour to start? What was the consistency of your flour before you added more? Did it have some resistance?
I made this today and the only change I took out oil and used applesauce. So my recipe was a full cup applesauce total. They were fluffy and awesome.
Love that, Annette! Thank you for your review.
Hi! I’d really like to try your recipe.Do you think I can replace the greek yogurt with cottage cheese?
That sounds interesting! I haven’t tried it, but would love to hear if you do.
I have also lot other ingredients except apple sauce. What can I use as a substitute?
What i can i use instead of greek yogurt (thats the only ingredient i don’t have)?
Apples are hubby’s favorite fruit, so was looking for a good apple muffin recipe. I made your recipe today in a dark Texas sized 6 muffin pan & used the same oven temperature and time. They came out perfect. My only substitutions were Honeycrisp apples and grapeseed oil. I used maple syrup and topped them with raw sugar. Very satisfied sweet tooth here! Made the house smell divine. Thanks so much for this recipe!
You’re welcome! Great to hear you loved them so much.
I’ve been addicted to these muffins for a couple of years now! I eat 2 every morning. It’s like healthy cake for breakfast. I make them vegan by substituting the yogurt with almond yogurt and substituting an avocado for eggs. Thank you for making my breakfasts healthy & delicious!
I love that! Thanks for sharing how you make them vegan and work for you.
Hi Kathryne
Thank you for the recipe. Your instructions call for eggs, but the ingredients list do not have eggs. Just thought I should let you know.
Cheers
Valerie
They are in there, see step 3. :)
Hi Kathryne
Sorry my bad, I must have skipped reading the recipe, the ingredients did call for 2 eggs. Thank you.
Cheers
Valerie
No worries! Thank you, Valerie.
Hi Kate
I made these this afternoon absolutely great. Thanks for the great recipe. I did add about 1/3 cup cranberries. I will be trying the blueberry, banana and raspberry muffins soon. I did think using coconut oil would add another taste dimension but you don’t even notice it
You’re welcome, Ian! I appreciate the review.
Absolutely love this. I swapped half of the flower with oats which worked out well.
Thanks for your review, Sylvie!
What can you use instead of apple sauce?
….?? She literally said in the recipe that she cut the greek yogurt with applesauce. Use greek yogurt.
Can I use spelt flour instead or wholemeal??
I haven’t tried it, sorry! Typically it doesn’t work as a 1:1 for me. But if you try it, I would love to hear that!
I love this recipe! I used two cups grated apple as my 3 year old doesn’t like chunks of things in muffins (very annoying!) and pear apple puree as that is all I had and they were light and fluffy and delicious. I usually keep lunch box sized apple sauce around for baking too but ran out without realising it! In the future I will try adding some oats and maybe more spices (or more cinnamon?) but that would be to appeal more to adults than to my kiddos who will love these.
Thank you for sharing, Sydne! I’m glad you were able to make this one work for your family.
Okay, it needs to be said that this is the BEST healthy muffin recipe ever. I use it as a base for pretty much every baked breakfast-y muffin thing i can think of…. and i throw in oats and some kind of vegetable (carrot or zucchini all depending on what I’m throwing in them that morning). MY KIDS LOVE THEM!! My 3 year old eats about 4 things, but with these muffins, she’s getting some sneaky protein and vegetables in there.
Thank you for existing and upping my toddler game! (As i write, they’re in the oven right now… and i know I’ll scarf down at least 2 before anyone wakes. )
Well, I’m glad you said it! :) Thanks for sharing, Stephanie. I’m excited they are a hit with your family.
These are crazy good. I’m not a big muffin fan, but with the apple sauce, the grated apple AND the diced apple – these are incredible. They are lightly sweet and moist and actually taste like apple. Thank you for this!
The only thing I did different was use 1 cup whole wheat flour and 3/4 cup White Lilly flour, since that I what I had on hand. I think it helped make these muffins very… light?
I’m glad you loved them! Thanks for sharing, Sarah.
Excellent recipe Kate, it’s a keeper. Thank you for sharing!
I’ve made this recipe twice, a double batch both times.
Laura, who commented below asking about adding oats, and Chris who asked about subbing out Applesauce – I hope you get to read this:
Instead of the 3 and 1/2 cups of whole wheat flour in the 2x version of the recipe, I used 1 and 1/2 cups of whole wheat chapati flour (because I’m Indian and have it lying around :) + 1 cup buckwheat flour + 1 cup porridge oats ground up (not too fine).
Instead of the applesauce (which I don’t usually keep in my pantry, being in NZ :), I used the same measure of yoghurt, in addition to the amount of yogurt already in the ingredients, thus doubling it.
I use a little less than a cup of maple syrup (so expensive here!) and trying to watch the sweetness as muffins will mostly go into kids’ lunch boxes and will just about last a week.
I’ve got a batch in the oven right now, and today in fact, I’m using berry yogurt that I had in the fridge instead of plain so let’s see how that turns out!
Thank you again Kate!
Cheers,
Radhika
Thank you for your comment and giving extra feedback, Radhika!
Hi
Would pear work instead of apple? I have a heap of pears to use up.
You could try it! I would go for less ripe pears that still have some bite to them to mimic apples closer.
I would recommend a lower temperature with a longer bake. Mine turned very very dark on the bottom with the apples still being slightly crisp. I’d go 375 for 20 minutes.
I’m sorry to hear that! Was your rack placed in the center? It could be your oven cooks a little hotter. I would maybe check on them sooner, rather than adjusting the temperature.
I baked today, and I am so happy for the result! Its so delicious!! Not dry but soft inside! The raw Sugar is perfect for sprinkling , it makes the muffin crispy on top! My son Love it and even my husband, who does not eat muffins! He had even two! Thank you for such yummies muffins Kate! Love them!
You’re welcome, Eva! Thank you for your review.
Can we have a substitute for eggs please?
Please see the notes under the recipe. I try to provide substitutions there when I can: MAKE IT EGG FREE: Use flax eggs instead of regular eggs.
These turned out amazing! I used apples that I’d already sliced and frozen from our trees last fall. Delicious, great way to use apples from our orchard!
Great to hear, Ashley!
I made these fabulous apple muffins today and they turned out beautifully. maybe not quite as high as what the recipe photo shows but they’re absolutely delicious! I ended up using the honey version and instead of using olive oil I used avocado oil; no added flavor. I will make these again and keep this recipe on hand they’re lower in fat and sugar compared to most muffin recipes and they’re better than anything you’ll buy at the store.
I’m glad they tasted so good! Thank you for sharing, Patrice.
Hi, I was looking for a vegan apple muffin recipe and your recipe came up. Looks delicious and I cant wait to try them. Have you made them without the eggs?
Hi Vicki, I haven’t but flax eggs should work.
Just made these and 6 are already gone, adult and kid tested and all loved them. Do you know the nutritional breakdown for these ? I am going to try the Poppy Seed, Lemon next and the banana ones too. So happy I stumbled on your site!!!
Hi Michelle! Unfortunately, my nutritional plug-in isn’t working at the moment and I’m working with my team to fix. I apologize for the inconvenience! Check back soon.
I have a bunch of almond flour on hand, would this work in the recipe? I’ve made your banana muffins several times and they are the best!
I wouldn’t recommend almond flour. I would suggest searching the comments to see what others recommend. They work great with a gluten free flour blend.
Great recipe thank you – I only had self raising flour, worked fine
You’re welcome, Meng!
Amazing!! Came back 5 mins later to only 2 left lol, I’m gluten free and sugarfree so I used gluten free sr flour, rice malt syrup and mashed banana for substitutes.
Amazing recipe Kate! Xx
I love that, Lily! Thank you for your review.
Hi Kate,
If I don’t wanna use applesauce, can I double up the yogurt instead? Aside from mash bananas which a fellow baker used, what’s feasible?
Thanks!
I have made this recipe twice. Delicious! It has become a favorite in my house. Thank you for sharing!
You’re welcome!
These were ok. My kids said they didn’t have much flavor, I have to agree.
I learned the hard way not to use paper liners! Luckily, I had made a double batch so the next dozen just went in the tin and came out perfect. Next time I would use pumpkin pie spice and use more, but I understand why she didn’t put a lot of cinnamon in, some people are really sensitive to the taste of cinnamon! So overall I’d say this is a great base recipe and make it your own!
Also! My double recipe made 36 smaller muffins, these don’t quite rise like traditional muffins.
I’m sorry you didn’t love these. Thanks for your feedback!
I did not like it, but my family said it was the best.
I’m sorry you didn’t love these, but I’m happy your family was able to enjoy them!