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
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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.
Oh my goodness, these are DELICIOUS!!! I couldn’t even wait for them to cool down before I popped one in my mouth. Glad to have stumbled upon your blog, Kate! I can hardly wait to try more of your recipes!
(PS., I used Jazz apples in this and – because I’m always looking for a way to add more fiber to my son’s diet – also added a spoonful of ground flax and hemp seed)
Saw your instagram post last week, looked at my pile of apples from my farm share (already?) and decided to make these muffins. They are so good! Just the right balance of healthy, tasty, & sweet, and I love the variety of apple textures. For breakfast, I sliced one in half, toasted it, and spread it with almond butter – yummm!
I make healthy muffins for my granddaughter to have for breakfast and/or lunch. Made this recipe for a second time with McIntosh Apples, substituting more apple sauce for cubed apples since she doesn’t like the smushy part, coconut oil, honey, a tablespoon of flax meal, a 1/2 tablespoon of hemp meal, lower/longer cook-time and threw in a handful of dark chocolate chips (good for you!) to make it more tempting. The only problem with these is, everyone in the family eats them up really fast :-) !
Great recipe! I made it for Rosh Hashana, the Jewish new year’s holiday, as we ritually eat apple and honey to wish for a sweet new year. It came out PERFECT and delicious! and thanks for the honey comment, It was very helpful.
They were great! I used 1cup almond flour and 3/4 white (no wheat in the house). So easy to make and yummy. It didn’t even need the sugar topping.
Wow
I really really love healthy receipes. I hope that you will have more and more healthy receipes
Oh. Could i use only baking powder
Thank you so much
No, it’s very important to use the leaveners called for in baked goods. Please stick to the recipe!
These are absolutely amazing muffins. I’ve tried many recipe’s, and I love your methods for creating these muffins.
They were SUPER moist, fluffy, and delicious. I took them to work and shared with my colleagues.
I used plain white flour instead of the wholemeal flour, and it worked well. The mix was probably runnier than it should have been but maybe that attributed to their moisture level.
I’m going to make this one again and put chopped walnuts in it for some crunch.
Really enjoyed these! Just the right amount of sweetness. Thanks!
Could you make these without applesauce? I love your other muffin recipes and I’d like to try to apple ones! I rarely have applesauce on hand, though. Thanks!
Hi, I actually like to keep mini (lunch box-sized) containers of applesauce on hand for the rare occasion that I need it. You could probably replace it with an equal amount of yogurt. The final result will not be as strongly apple-flavored.
Could I substitute self raising flour for plain/all purpose? That’s all I have left in wholemeal/wholewheat in my pantry! Would I leaves out the baking powder and baking soda in this case! Thank you!
I’m sorry, self-rising flour isn’t suitable as a substitution. The exact amounts of baking soda and baking powder are key in this recipe (and all other baked goods). It’s highly unlikely that you’d get the proper amount of each in a pre-mixed self-rising flour. Sorry to disappoint!
Hi! I was just searching for recipes to use the bounty from our apple picking trip and this looks terrific. I have a question though – my boys love apples “raw” but they don’t like them cooked (“too mushy”) so I’m making a ton of fresh applesauce now and will use that instead of shredded or chopped apples. Any idea how much fresh applesauce I’d need? Just add up all the apple and applesauce quantities and use 2 1/2 cups? Thanks!
Hi Lisa, I’m sorry I didn’t see your question sooner. The apples here are cut so small that they don’t really get mushy like other baked apples. That said, I’m not sure how to answer your question since extra applesauce will likely introduce more readily-absorbed moisture into the recipe. Please let me know how it turned out if you gave it a shot.
My toddler, husband and I are huge fans of your pumpkin and banana muffins but now that we’ve tried these apple muffins we might have a new favorite! They are AMAZING! And healthy enough to be enjoyed for breakfast (without inducing a toddler blood sugar spike!) or just sweet enough for an after dinner treat. I have a feeling we will be making a batch of these every week for the rest of fall.
We went apple picking this past weekend and I made these for my family. The pickiest child rated them an “A+”. My husband couldn’t believe there is no sugar in them. Super moist and just the right amount of sweet. Thank you!
Question: Do you think I could make this recipe as a bread loaf? I can’t find a comparably healthy recipe for apple bread! Thanks again!!
These turned out so light and fluffy. My batter seemed to be a little wetter than yours but I just baked a little longer. The only change I would make next time is to add a little more cinnamon.
Absolutely delish! I recently made a huge lifestyle change and this was a perfect fit! I will be making these again and have saved the recipe! Thanks so much for sharing!
Thank you, Hannah! I am happy to know it works well with your new lifestyle change and that is will be a repeat!
Can I replace the Greek Yogurt with Buttermilk? I know it doesn’t really make it healthy but I have some left that I want to use up so… was hoping I could use it here? Thanks!
Hi Connie, I think you could! Just use slightly less buttermilk than the amount of yogurt called for here. And don’t feel bad, buttermilk is not an ingredient I would consider unhealthy! :)
Thanks for making me feel better about the substitution. I did switch it up, buttermilk for yorgurt and it turned out well. Phew! Did about the same amount as the yogurt. Will have to try again with the yogurt to so I do a proper compare but I was happy to get rid of the excess buttermilk I had.
I am always happy to find recipes online that are made healthier without being dull from dishes or sweets I love! It’s my first time making muffins with apple. That’s why I’m wondering if they are supposed to be so moist? I made muffins with blueberries before which were not as moist. Is it because of the amount of apples or the applesauce?
Just wanted to say that after the muffins cooled down completely they were perfect (not so moist as I found them straight from the oven)! My flatmates and me loved them so much that I will repeat this recipe again very soon!
Hi Kate! Made this recipe tonight and reaped my reward with some ahmaazing apple muffins, so firstly.. thanks a lot! And here comes my question: since I halved the recipe, I was a bit uncertain regarding how to adjust the bake time.. so I ended up just, uh, kinda winning it. Got any advice for how to adjust for someone with a 6-muffin pan?
So glad your muffins turned out well! If you have a 6-muffin pan and the recipe yields 12 muffins, just divide the amounts by two and bake for the same amount of time specified in the recipe… I think that will work! (I say this assuming that you’re muffin pans makes regular-sized muffins, not jumbo, in which case the muffins would take longer to cook.)
Hi Kate, I will make these muffins tomorrow..but I need to double the recipe…can I do that or do I have to make two separate batches? Plus do you know how much sugar and carbohydrates are in each muffin?
Thanks.
Marj, you will be ok just doubling and dividing up the batter to an additional 12 muffins. The nutrition information below the notes section provides the estimate for the serving size, which is one muffin. Hope this is helpful!
I love this recipe I am in the kitchen manager for a senior living facility for trying to make healthy food are used coconut nectar as the sweetener the residents all loved Them the muffins looked beautiful and thank you for all the lovely recipes on your site
Made these muffins last night and there are already only 6 left! These muffins are delicious, so moist and perfectly sweet – great recipe! Thanks for sharing :)
You are very welcome, Kelsey! Thanks so much for sharing and for your review :)
Thank you for this delicious recipe!, Made it over the weekend and the whole family loved it!. Definitely a keeper.
You are welcome! I am happy you enjoyed it Edith :)
What could I replace the apple sauce with? Living in Uganda and apple sauce is not easy to come by!
Hi Ruwani, I would probably replace it with an equal amount of yogurt. Hope that helps!
Wonderful! I’d give it more starts if possible!! This recipe is so flexible; the 2nd time I baked them, I added more spices, sub’d brown sugar for maple syrup, and omitted cubed apples. They still turned out incredibly moist and flavorful and were nicely domed. This recipe should be in every baker’s repertoire! Thank you!!
You are so sweet, Kathy! Thank you so much. :)
Full of flavor! Mine stuck to the paper muffin cups I used, but they were still delicious! I added a tsp each ground flax, chia seeds, & some Amazing Grass powdered greens to the mix & you couldn’t even taste all of the extra healthiness. LOL
Thank you for making another way to enjoy healthy & amazing muffins!
Wondering though, where I might find the nutritional info?
I am happy you enjoyed them Diana! The nutritional information is under the recipe notes section. You will need to click to expand.
I made these last night with the vegan and gluten free substitutions you suggested — they were fabulous! A bigh THANK YOU for sharing this. Its so hard finding healthy vegan and gluten free recipes and this fits the bill perfectly.
That’s great! Thank you, Shellie.
Oh my goodness, these are so delicious. The whole family, including my 1-year old will love these for breakfast. I used half granny smith, half gala apples for a nice tart-sweet balance. Will definitely make again!
Thank you, Danielle for sharing! I really appreciate the review. :) I’ happy your kiddo will love these for breakfast.
I used double the applesauce instead of adding Greek yogurt and they turned out great! I also added in walnuts. So delicious.
Thanks for sharing, Alaina! I’m glad they turned out so well for you. :)
I am looking to make a completely sugar free muffin. (This means no honey, no maple syrup, no agave, etc… no sweetener!) Can you recommend a substitute for the honey? Or can I just omit it? The muffins need not be sweet, I just want don’t want to throw off the batter. Would something like mashed banana work?
Hi Barb, I think mashed banana is probably your best bet.
Absolutely delicious! Used a Granny and Honeycrisp, turned out fantastic.
Your recipes NEVER fail to please!
Lovely! Thank you, Linda. :)
I first found you because of your healthy, yummy muffin recipes! This is one of my favorites. Fluffy and delicious.
How many calories do the healthy apple muffins have?
A stormy morning here , but it’s perfect for something warm from the oven. These muffins fit the bill and we’re delicious and moist ! Thanks Kate & Cookie. Loving the cookbook !
A perfect baking morning! Thank you for the comment and review, Elizabeth! Happy you loved the muffins.
I do not show the nutritional value. I click on the arrow and nothing shows.
Just making my second batch because the first one was so good (and didn’t last long!)
Thanks for a healthier version of muffins.
(Trying to rate it 5 stars, but 1 star keeps disappearing)
That is a great problem to have! Thank you for the review. (That shouldn’t be happening, so I will look into it! Thanks for letting me know).
I made these this morning with my 6 and 11-year old. I doubled the recipe and used half pure maple syrup/honey and half yogurt/apple sauce. They were delicious! Every one loved them and they made the house smell wonderful on this crisp spring morning. Thank you for sharing your talent!!
You’re welcome, Camie! I’m happy it was great for the whole family.
wow, it looks so incredible and healthy, my husband and son would love this. thanks for the recipe.
You’re welcome!
Could I use Kamut or Spelt flour? My husband is wheat sensitive so I try to use ancient grains.
Made these April 2,2018 Temp 350 -Honey Unless Noted all Ingredients Same
1 1/2 tsp Cinnamon, Green Apples,3/4 c Honey, Sour Cream (in fridge), Pureed Apple = Applesauce, 1 1/2 tsp Vanilla, Cinnamon Sugar on top.
I LIKE these But, Husband Wants at least 1 Cup Honey with OUR Sour Apples.
I will make these again with MY additions.
THANKS for Posting.
You’re welcome! Thanks for sharing.
Okay these are so freaking tasty. I’ll be lucky if they last 3 days. Adding to my recipe box :)
Wonderful to hear, Sydney! :)
Can I susbstitute the apple sauce for coconut oil?
Unfortunately no. Sorry! You can use olive oil.
Can I use butter in place of the coconut oil? I don’t have any oil on hand and it can be so expensive!
what is the purpose of the greek yogurt? can it be omitted?
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.
I look forward to trying this recipe. When I click on nutrition it doesn’t show any stats. I am a weight watcher and need fiber, carbs, protein and fat. You know it might make the difference between having that second muffin with my coffee. Thank you.
Sometimes browser settings will blog the plug-in. Try clearing your cookies and allowing pop-ups if that doesn’t work. Hope this helps!
I found that when I went to my phone rather than my computer the nutrition stats popped up. Five points per muffin. That’s about the points for most healthy muffins. One that I get from Whole Foods is 8 points so 5 is good. I have done the point system for 8 years. For me I need the accountability. Can’t wait to try these. Thanks
These muffins are amazing! I’ve used oat flour instead & that works great. I’ve only peeled the shredded apple & leave the skin on the chopped which makes a nice combo. I highly recommend this recipe! These muffins are close to perfection on flavor & nutrition.
Wonderful, Greg! Thanks for the review.
Can I substitute whole wheat pastry flour?
Specifically, I want to use Arrowhead Mills Organic Pastry Flour.
Hi Claire, I think so. The muffins will be a little more delicate and your batter might be more wet, but I think your muffins will turn out well!
Thank you so much Kate. I’ll be trying the recipe soon.
I love your recipes. I have a serious sweet tooth and your recipes have provided me with a great opportunity to cut back on the refined sugars and still enjoy all the yummy baked goods.
This is a very forgiving recipe! I changed it considerably and it turned out amazing. Used extra apple sauce instead of chopped apples, gluten free self raising flour, left out the baking soda as I had none, used rice malt syrup instead of honey and it still worked so well. Thanks for an amazing recipe.
Thanks for sharing, Emma! I appreciate the review.
These were amazing! Lightly sweet, very moist, and they feel so great to eat (versus the sugary unhealthy ones you buy at the store). I used honey instead of maple syrup, and it worked wonderfully. I would say maybe I’ll add a little more cinnamon next time because I love that spice, but honestly, best muffin recipe ever. Now I have to try the others – can’t wait! Thanks Cookie and Kate! :)
I’m happy you think so, Samantha! I appreciate your star review and comment. Let me know what you think as you try the other variations.
Can I replace the oil with apple sauce?
Hello to Cookie and Kate,
I have been making you wonderful muffins for our boys they loves them, as they are watching what they put into his body and your healthy muffins have hit the spot.
I love having to use a recipe that works.
AWSOME!
YUMMY
DELICIOUS
MARVELLOUS
Next pay packet I am going to purchase the cookbook.
Thank you both so so much!
Love from one happy family.
Souflas family.
❤️
I love all of those words, Alexandra! Thanks so much for your review.
Which of your muffin recipes would you best recommend for kiddos and which would freeze best? Thank you!!
I don’t freeze all my recipes, but I recommend looking through the comments to see other readers success. :)