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.
Just made these as mini muffins, baked for about 13 mins at 325F and came out absolutely perfect! Love the texture of both the grated and diced apples. Used whole wheat flour, honey and low fat plain yogurt. Hands down the best healthy baked good I have ever made! This one is a keeper!!!!
Thanks, Lakshmi! I love seeing all the variations my readers experiment with. I’d have a hard time eating just one of those :)
Does it have to be in muffin form? Or could i bake it in like a bread baking tray?
I’m sure you could, though you’d want to adjust the timing and temperature. Here’s a good article to help with adjusting from muffins to quick bread.
I have already made it 3 times. It is so amazingly moist and yummy. And there is no guilt feeling either coz it is so healthy! LOVE IT!!!!!!
Thanks so much, Ashima! So happy you loved them.
AMAZING recipe! I’m always on the lookout for healthy muffins that I can feel good about feeding to my toddler, and these are so tasty and moist that I feel like I’m totally indulging myself too!! Also, they make my house smell incredible. Thank you!
You’re welcome, Kirsten! I love that these taste like a special treat, too.
These sound great! What could I use instead of applesauce (or could I just leave it out?), and do you think I could freeze these? Thanks!
Hi, Rebecca. The applesauce could be replaced with mashed banana if that’s what you have on hand. These should freeze just fine, if you’re looking for an easy grab and go breakfast. Thank you!
BEST MUFFINS EVER ! Since finding this recipe about a month ago, I literally have had to make them 2-3 times a week because they only last a day in my house. Everyone from grandpa, to my 1 and 3 year old devour these. I share them with everyone at work and have forwarded the recipe to all my friends. Whats not to love… no sugar, two full apples, (i throw in raisins) and MAPLE SYRUP .. yum. THANKS FOR THE RECIPE !
Oh, raisins sound like such a tasty addition! Thanks for the kind words, Sarah!
These are amazing! I ended up using 1/4 cup honey and 1/4 cup brown sugar as I am running low on honey. The dough was a little thinner than I thought it should be based on your instructions (probably because the apples I used were quite juicy!) so I threw in 1/3 cup quick oats to thicken things up. They turned out great! Two down already and the night is still young :)
Thank you for making recipes that are so amenable to adaptations. I have tried a few of your muffin recipes (and made each recipe MANY many times), and while I’ve always had to modify the recipe slightly to reflect the ingredients I have on hand, the muffins are unwaveringly amazing, every time.
Thanks, Elle! I love that they’ve been adaptable enough for what you have on hand.
Just made your Apple Muffins this morning. They are wonderful. I used coconut oil as opposed to olive oil, and it gave the muffins a really nice flavor. Thank you for all your inspiring recipes.
Sounds delicious, Ellen. :)
Didn’t see any nutrition information. Are there any?
Fantastic! Best apple muffins I’ve ever made. Thanks for the recipe!
Awesome!! Thank you, Stephanie.
The apple muffins were very moist. I used egg whites instead of whole eggs and honey instead of maple syrup.They will be good for breakfast. Do you have the nutritional value for these muffins ?
Hi, Patricia! Unfortunately, I don’t have nutritional info available for my recipes just yet. I’m looking for a solution, and will update about it once I find one. Thanks!
5 stars from a picky 4.5 year old!!! Can’t wait to try some more of your recipes I stumbled across this when I googled healthy muffin recipe. Thanks for posting!
Great! So happy everyone loves it, Kristi.
I made these wonderful muffins today, after making and loving, your banana muffins. They turned out perfectly. I really enjoy a good muffin and one made with healthier alternatives is perfect. The only substitution I made was subbing avocado oil for the coconut oil. I use, and love, coconut oil but in baking I prefer avocado. Thank you for your wonderful recipes. Good luck with your cookbook!
Thank you, Lesley! I’m so glad you enjoy the muffin recipes.
Made these today for my 2 year old. He loves them! I used silicone mini muffin cups and baked for 8 minutes. It made about 40 mini muffins.
Yum! Thanks, Jennifer.
Made them as soft and chewy cookies; light and delicious!
Oh, what a great idea! Thanks, Florence.
Just popped these in the oven! I had forgotten the cinnamon in the batter so I mixed maple flakes and cinnamon to sprinkle on top!
Can’t wait to give these to my littles when they get home from school!
Thanks for a great and healthy after-school snack!
You’re welcome, Jennifer! I hope these get gobbled right up. :)
I love these muffins. I have to say I made these because I have some past their prime apples kicking around my kitchen.
This recipe is an experimenter’so dream: I didn’t have any yoghurt… Mostly because I’m allergic to milk. So, I took your suggestion to use almond milk with vinegar to make buttermilk. I also only had one egg in the fridge. So I substituted one vegan egg and used one regular egg. Plus, I used a mixture of maple syrup and agave for the sweeteners. I also didn’t want to run out and get wheat flour, so I used a mixture of chickpea flour and regular white flour. I so wish that I had wheat flour, but the result was fine. Chickpea flour adds heft and a good crumb. Oh, one more thing– I had to make my own applesauce because I didn’t have any of that either. (Made it with a red apple) Can you believe that these turned out? They are yummy and apple-y and not too sweet. I will come to this recipe again – – especially when I have the right ingredients. LOL. Thank you.
I didn’t have any apple sauce or yoghurt so I put in smashed banana, some milk and oats and they turned out great! Also I used honey instead of maple syrup. Thanks for the recipe!
These muffins are amazingly delicious!! I used dairy free cashew yogurt. My seven year old nephew said they were the best muffins he’s ever had :)
Hooray! Thanks so much, Brett.
I had a ton of apples to use up and was looking for a good healthy snack for my kids besides making applesauce or just cooking them with cinnamon. These came recommended by someone in a healthy eats group I follow. I made them as directed, but did add in some more cinnamon. I used honey, and baked 24 mini muffins at 325 for 20 minutes, and had enough batter to make 6 regular size muffins baked at 325 for 25 minutes.
I froze half the batch for later and will have a nice breakfast treat for everyone tomorrow. Thanks for the great recipe!
That’s wonderful, Kristine! These are a great grab-n-go snack. I hope the kiddos enjoy!
Hi Kate!
I’ve tried a few of your muffin recipes and they always turn out great! For this particular recipe, I used pink lady apples and they were delicious! However, I’ve gotten a few comments from friends and family about the distinctive taste of olive oil in the muffins (I used extra Virgin because its what I had at home). Other than the coconut oil, do you have any other suggestions for substitutions? I wouldn’t mind if they were slightly unhealthier options :p
Thanks!
Lavanya
Hey, Lavanya! I’d definitely try grapeseed and avocado oil instead of the olive. They have a milder taste, and should work well with the sweeter flavors of the muffins. Let me know how it goes!
I am quite impressed! These muffins are great! Moist, cake- like texture! I will definitely make them again!
Awesome!
I discovered half way through I didn’t have any good apples, but the muffins were still delicious without them!
Oh no! I’m glad it still worked out, Sue. Thanks!
Delicious! Especially for a “healthy” muffin. I used spelt flour instead of whole wheat as I’ve found it results in a lighter texture and better flavor, even though health benefits are the same. Also used about 3/4 C applesauce and finished the cup off with light vanilla soy milk instead of yogurt (because that’s what I had on hand, and also wanted to keep it vegan). And, I used the vegan flax eggs instead of real ones. Love the combo of shredded and chunks of apples (I used Fuji). I also used melted coconut oil and pure maple syrup. SO GOOD. Best muffins – and easy – the entire process took only about 30 min.
It’s great to hear that these worked out so well with those swaps, Mary. Thanks so much! I’m sure this comment will help another reader who finds themselves in a pinch and needs some tips!
Okay, I’ve tried four of your recipes so far and every one has come out perfect! That makes me a Cookie+Kate convert! I used coconut oil and soy milk with the suggested addition of a bit of vinegar. I really needed to eat healthier for breakfast. These and your variations will be staples for breakfast options . . . but great for on-the-go snacks as well! Your scones are next . . . :)
Hooray! I’m so glad you found my blog, Koriander. Let me know how the scones go!
Ive never reviewed anything but these were so delicious. I used honey and didn’t have any baking soda so added another 1/2 tsp baking powder. I only had peach carrot apple sauce and you can’t even tell. For the topping I used brown sugar mixed with cinnamon. They came out amazingly moist and the topping added just the right sweetness. I baked them at 325 for about 35 min. This will be my go to recipe from now on. Two thumbs up!!
Thank you, Felicia! They sound delicious.
Very moist, cooking time was 5 min more, very tasty. I used grapeseed oil and my own apple sauce. I realy like the cube apple for the added texture. Did not used sugar.
I’m so glad you enjoyed this, Michel!
amazing! third week in a row making them! ive easily added an extra apple to the mix as well as some walnuts or pumkin seeds to add protein! love them
I’m so glad you love these so much, Alex!
I just made these and they are delicious!! Does anyone know the nutritional information?
Your “Healthy Banana Bread” is my go-to via a google search last year. Searched for a muffin recipe for a potluck breakfast tonight and found these. They’re in the oven now and I know they’ll be nothing less than spectacular. Bonus: I love that there will be something there for my family that isn’t going to be junk! :) Can’t believe I haven’t browsed your site before. Excited to try more! Thanks Kate (and Cookie)!!
These muffins are delicious! I added raisins, oatmeal and sprinkled brown sugar on top. Perfect!
Thanks for sharing this awesome recipe. I look forward to making another batch.
Made these today with regular whole wheat flour.They were light and fluffy. Thanks for the recipe.
Great! Thanks, Ramya.
Made this with oat flour, maple syrup and plain Kefir. It was a hit a work and home! Thank you!
Yum!
Can this be made into a loaf if I follow the instructions and bake for 50ish minutes?
Yes! Baking between 45-50 minutes should do the trick.
Awesome – can’t wait! Your book came in the mail today — Looking through it now. So many amazing recipes I’m looking forward to trying. And I love all the “extra” information. So helpful – what a great resource! And the photographs – just beautiful.
Yum these turned out wonderfully! I used red delicious apples, sunflower oil and maple syrup!
Yum is right! That sounds delicious.
This recipe is amazing it is so yummy and usefull for us (cause we have heaps of apples on our tree) thanks Kate
Plz reply!
Wonderful! Thanks, Hannah!
I made these muffins with no sugar or syrup. I used a teaspoon of stevia but it probably wasn’t necessary either. I made them smaller and made 18. They worked out well.
Great! I’m so glad you loved them, Kirsty.
What is the nutritional content on these muffins? I made them and they are great. But I wanted to know the approximate fat,calorie content, ect. per muffin?
Hi, Dana! Unfortunately, I don’t have nutritional info available for my recipes just yet. I’m looking for a solution, and will update about it once I find one. In the meantime, here’s a nutrition calculator that might come in handy.
Fantastic! These are absolutely delicious! They came out perfectly and all my neighbours loved them.
Wonderful! Thanks, Deanna.
These just came out of the oven and oh my goodness they smelled so good I had try one right away. I cut one open put a tiny pat of butter (don’t judge). Hands down the best tasting muffin I have ever had in my life. Perfectly moist not too sweet just incredible. My four year old will love waking up to these for breakfast in the morning. Thank you!
Hooray! I’m so glad these made such a good impression, Kara. :) Enjoy those muffins (with butter)!
My partner and I are on a health journey and I was so happy to come across this! My partner has a massive sweet tooth and there was so much joy as she ate these! They are perfect and guilt free! I made with red apples because it was all we had and still perfect! I misread the raw sugar for brown sugar on top but still yummy! I’ll definitely be trying your other recipes
Great, Harmony! I’m so glad the two of you enjoyed these. It’s a good antidote for a sweet tooth!
YUM! I made these last night so that I could have a special breakfast treat on a Saturday morning. They were so moist and delicious! I did need to add about 3 minutes to the total baking time because they were too wet at the 15 minute mark. My hubby kept saying “these muffins are soooo good” and I’ll definitely make these again. Thanks for the terrific recipe!
Great! I’m glad they came out well, with just a little extra time. :)
Is like to add some almond butter to the recipe; do you have any recommendations for how much and if that’ll change the consistency too much?
Hi! I saw your comment and thought I’d let you know that while I didn’t put almond butter in my batter, I did, once the muffins were cooled, cut some in half, toast them, then spread with almond butter, and it was delicious!
Toddler approved recipe , I’m being nagged for another. Used rice malt syrup instead of honey/maple and left the apple sauce out as it’s not a staple here. Turned out perfect !
Haha! Glad to hear the kiddo enjoyed these.
I just made this apple muffin recipe and must say that I really like it! I skipped the sugar and used only maple syrup. I also had to add a half cup of oatmeal flour(just ground oat flakes) because it was a little light after adding all the ingredients. Thanks Kate for sharing this recipe! Cheers, Teddy
Hi, I really want to try your muffin recipes, this one especially! By twin boys will turn 1 soon and I want to make a small cake for each one. Do you think the muffin recipes will work as well if I put the batter into a cake pan? Thanks!
I made TWO batches today to freeze for kids snack packs (made 29 in total)! Tasted some before they went into the freezer of course and they are so fluffy and delicious! I followed the recipe but added soft raisens, a teaspoon of mixed spice with the cinnamon & sprinkled organic coconut sugar on top instead of turbinando sugar. Absolute hit with the family. Kids wanted more and I kept saying “Stop eating them! They are for your school snacks!!” Hahaha
I collect muffin recipes, and this one has just gone straight to the top of the list! It is now our family favourite! I am writing from England, and I used traditional English apple varieties: Bramleys for the applesauce, and the Cox variety for the cubed and shredded portions. The maple syrup came from my family’s farm in Canada, so it was truly an international production! My four working Border Collies enjoyed the crumbs, and send their best regards to Cookie. Thanks so much for a fantastic, truly creative recipe!
Oh, I love this, Louise! Your muffins sound delicious. Cookie says hello to your four pups! Give them some pats for me. :)
I made these exactly as written and quite enjoy how they turned out in taste, texture, and easieness to make. I keep them in the fridge for a quick snack here and there and will surely make them again. Nicely done. :)
Perfect! Thanks, NeeNee!
Hi Kate! It’s apple season and these look amazing! I made them this morning and opted for honey instead of maple syrup. I adjusted cooking temps and times as noted; however, they still came out rather wet. I measured dry ingredients with dry measuring tools, and wet ingredients with liquid measuring cups. I did bake them in silicone muffin liners, and wondered if that had anything to do with it. Any ideas where I went wrong? Thanks for all your delicious recipes!
Oof, oh no! Sorry about that, Sharon. A couple things could have happened: did you switch the baking soda and baking powder proportions? When things come out wet still, it’s usually a powder/soda mixup. Since this recipe includes both, it can be easy to switch them. Also, some apple varieties are juicier than others, so you might need to squeeze out some of the wetness before adding the shreds to the batter.
Excellent ideas, I’ll have to try again. It could be the apple variety (picked them off my tree). They look/taste/smell like McIntosh, but I’m not 100% sure. I also forgot to mention I used flax eggs in place of regular eggs. I think I’ll retry the recipe and go with the maple syrup, regular eggs, and squeeze dry the apple shreds. Wish me luck, haha! Thanks again!
These were tasty. Nice texture too. I used a combo of Fuji, gala and mac. Half honey and half maple syrup. As the only Greek
Yogurt I had was lemon flavour, I used half that and half regular plain yogurt. It made 12 muffins about the same size as in the recipe photos and 6 mini- muffins. These will be great as work-lunch snacks.
I did give these four stars in my first comment! Lost a star somewhere!
Perfect! They sound delicious, Robyn. I love trying these with new combos of apples.