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.
I went apple picking and was stressed over how to use all of the apples – fresh applesauce and a few batches of these muffins did the trick – they are delicious! I used Bob’s Red Mill Gluten Free flour and they turned out fine. The Greek yogurt adds great flavor.
Thank you, Anna! I’m glad you came across my recipe. Now I want to go apple picking!
Could I possibly use almond flour of coconut flour instead?
I’m not sure how well those will work, but I know that Bob’s Red Mill’s gluten-free flour blend works well.
Is there anything i can use in place of the greek yogurt? Thanks in advance!
Yes, I have a tip for that hidden in the vegan notes at the end of the recipe. I will try to make it more apparent!
These look delicious and I definitely like the idea of a healthier muffin. Apples and cinnamon are such a comforting flavour combination. I wondered what could replace the Greek yoghurt? Dairy doesn’t agree with me so I’d be keen to make these with an alternative – could I double the apple sauce?
Hi Amelia! That’s a good question. I have a dairy-free suggestion with non-dairy milk and vinegar (to turn it into buttermilk) hidden in my “how to make it vegan” note at the bottom of the recipe. I’ll try to make that more clear for other dairy-free visitors!
Thanks Kate! I should have read the little notes more closely!
These looks amazing – apple and cinnamon are a great comforting combination. I was wondering if it would be possible to replace the yoghurt with more apple sauce? Dairy doesn’t agree with me and I am hoping I can still make these for myself!
I made these this morning and I used whole wheat pastry flour and it turned out great. These are not too sweet and very moist. Loved them – thanks as always for great recipes.
Hooray! Glad you enjoyed the muffins, too.
I made a half batch of these wonderful muffins, and I’m glad since they are so good I’d eat too many if there were the full 12. I have to say they are among the yummiest muffins I’ve made (and I make a pretty darned good banana nut muffin).
I happened to have all of the ingredients in the recipe except for the plain Greek yogurt. I used plain whole milk regular yogurt and it was just fine. I used the coconut oil for the first time in cooking and bet that really contributes to the lovely flavor. [Actually my husband bought it to use to moisturize my parrot’s feet, but it was organic and food grade so I gave it a try.] I chose to use maple syrup since I had more of that on hand than honey. I used Jonathan apples since they bake well, taste great, and were fresh picked by my husband and I from the orchard. This recipe is a winner. My husband is going to LOVE them. He is a major apple fanatic and loves muffins too.
Hi Cyndee, I’m so glad you’re loving these muffins! I bet they were extra delicious with those super fresh apples.
These are some of the fluffiest, most apple-icious muffins I’ve ever tasted! Made them with half KAF gluten free flour & half oat flour. Came out amazing!
Awesome! Thanks, Amanda!
I just discovered you! Cookie is adorable. I am a dog lover. Ok your zucchini bread is in my oven baking now. I am thinking of making your apple muffins with the honey, coconut oil and applesauce next. Do you think I could make a bread with the same muffin recipe? Have you done that before? Also I have homemade applesauce I am thinking of using. What do you think? Should I live dangerously and try it?Your new follower, Nancy
Hi Nancy! Thank you for your note. I haven’t made apple bread from the apple muffin recipe, but I think that would work great. Homemade applesauce should work well, too. I would bake the apple bread for the same length as the zucchini bread, so 55 to 60 minutes, or until a toothpick inserted into the center comes out clean.
Thanks for this recipe, Kate! I used multigrain flour and subbed out the flax eggs for regular, and they turned out great!
Awesome! Thank you, Lavanya!
So delicious! Was looking for the perfect “healthy” muffin since I’m not eating gluten or sugar other than honey. Used King Arthur’s gluten free baking flour and these came out wonderfully. I did have to bake them a bit longer (about 30 minutes total) to get the toothpick out clean but they are soo good. I’ll admit I was a little worried with the 1/2 c of honey as I’m pretty sensitive to sweets, but it was the perfect amount. Thank you!
Thank you, Stephanie! I’m so glad you enjoyed these.
Just made these with apples we picked from the orchard. Soooo good. I made 13 muffins–lucky baker’s dozen. Love the earthiness that the whole wheat flour gives it, and I liked that I peeled my apples as they’re soft. Thank you, Katie, for sharing this recipe that’s perfect for fall.
Thank you so much for letting me know, Jessica! Now I want to go pick some apples. :)
Great recipe, used GF flour and turned out fantastic ! Will make them again!
These were amazing you’re the muffin queen! I make all your muffins and I’m never dissointed. So great knowing they’re healthy enough to give to my kids on those days we’re rushed for breakfast.
Thank you, Alison! I appreciate it. :)
These muffins were fab my whole family enjoyed these health Apple muffins and easy to make, many thanks !
Thank you, Pamela! Happy to hear it.
Just made these and they are absolutely delicious. I did make a few minor changes as follows: added allspice, used half white ww flour and half ww pastry flour and did half maple syrup and half sucanut.
The texture was perfect with the perfect hint of sweetness. They were easy to make and not very time consuming. I will definitely be making these again and again.
Thanks so much for the healthy recipe.
Thank you, Shanelle! I’m so glad you loved these.
Amazing recipe! I’m a sugar-freak, and my husband is a health-but, and we both loved them!
I’ve made these before and they’re delicious! BUT – I made them for the first time since going dairy-free and used soy yoghurt and they were just as amazing! They also work well with pear and/or raspberries if you run short of apple :-)
Hi Kate! How can I incorporate some oat flour into this recipe? Thanks!!
Just curious, how many calories are there in each muffin ??
Thank you there were delicious!
I didn’t have any apples. I substituted applesauce and they were delicious.
This is an excellent recipe with lots of apple flavor. We had a huge crop of apples this year so I am excited to find another great recipe to use. We love nuts so I did add some chopped walnuts otherwise made the recipe exactly like it says. I peeled the apples – wasn’t sure if the peel left on might be too tough. I will make this many more times this fall. Doubt if it matters what kind of apple is used. Thank you for an excellent recipe.
We have two McIntosh apple trees, so about this time every year I’m looking all over for ways to use our apple bounty. Tonight I made these healthy apple muffins with our apples, and they are delicious! And the fragrant cinnamon-apple aroma in the kitchen while they were baking was pure Autumn.
Wow these are delicious! Made them this morning for breakfast. User half Granny Smith and half gala. Not too sweet which is how we like them. Super easy to put together. Thanks for sharing.
Wow, these are amazing. Thank you for the recipe!!! My go to muffin from now on.
I made these recently and they were delicious! I made them gluten-free by using almond flour (added an extra 1/2 tsp of baking soda), I also added 1/2 cup of flax meal and walnuts. My 4 year old daughter helped me make them and she added chocolate chips to the top (I must admit that it was a yummy addition:-) The muffins were very moist and filled me up until lunch time. I am making another batch tonight. Thanks for the recipe!
I love these muffins! I’ve made 2 batches, the second with some pear and walnuts. Both delicious. Thank you for the recipe, I’m always looking for healthier treats that taste delicious for me and my family.
Hi!! Do you know what I can substitute the applesauce for please??
I’m curious do you have a nutrition guide for this recipe?
Made 2 batches. First one is super good. I love it. The second batch I made with a cannabis infused coconut oil, OMG its sooo good. It will allow you to talk to god, actually allows god to talk to you, be prepared cuz god talks way too much. Apparently he is always listening and never has anyone to listen to him, go figure.
Tasty! I made these this morning. I’ve never baked with coconut oil before – I measured out a solid 1/3 cup and melted that. Hope that’s the correct way :) I used just about 2 whole apples (jonagold and honey crisp) and the only thing I changed was I added was 1/2 tsp of pumpkin pie spice in addition to the cinnamon. My 3 yo son loved them. I love to bake my waistline is rapidly expanding. I’ve been looking for healthier options and this one is definitely a keeper. Thanks for the great recipe!
Kate I LOVE your Banana/Oats/Maple muffins but need something new! Can I add strawberries? Would they work? I want a *healthy* way to get more fruit into my son’s school day (even disguised!)
Thank you for this recipe! I made my first batch last week and they were delicious; light and yet full of apples. My kids LOVED them. I’m going to make my second batch today.
I just made these for my daughter’s school lunches but want to eat them all right now! Delicious! I skipped the applesauce (I didn’t have any) so did 1 cup of vailla yoghurt instead. Thank you!
can you replace the apple sauce with something? Maybe even apple juice?
How could I turn this into an Apple Bread Loaf? I’m obsessed with your Healthy Banana Bread recipe (I make it almost every week!) and would love to try an apple version.
Hi Mona! Sorry, I just saw your question. I would just pour the batter into a greased loaf pan and bake until the center springs back to the touch, somewhere between 40-55 minutes. If you give that a try, please report back with the baking time so I can share in the recipe notes!
Delicious! Moist, perfect amount of sweetness. I didn’t have applesauce and used a little extra yogurt and a few splashes of apple juice instead, and that came out great. I cooked at 325 as you said, since I used honey, and that worked great, too. Thanks for giving such great gifts to me and my family through your fabulous recipes! I am a huge fan and lover of every recipe I’ve tried on here!
Followed the recipe as listed using exact measurements but batter was “soupy”. I used organic whole wheat pastry flour, and I chose honey instead of maple syrup, therefore I followed the tip to bake at 325* for 25 minutes.
I just made your Healthy Apple Muffins, and they are perfect! They are moist, and delicious. Your recipes are so reliable and yummy. Always consistently excellent! I make the lentil soup recipe you posted at least once a month. It’s now a family favorite, and I’ve been asked for the recipe multiple times. Thank you for your work creating and posting these recipes. I just signed up for your newsletter, which will give me lots of inspiration! My kitchen smells so good, and we have this tasty treat to look forward to. Thank you! <3
I just made these, and they are delicious! So tender and flavourful.
I used Empire Apples & homemade Chile Applesauce, and added a touch of ginger!
Can i replace applesauce with something else ? :)
I make these muffins every week for my family and for children In my family child care. They are delicious!!!
Any idea the calories in these?
Hey, Sar – Right now I don’t have the nutritional info or calorie counts for my recipes, but I’m working on finding a solution soon.
OMG just made them and they turned out soooo delicioso. Moist and fluffy. I did not have apple sauce so just used yougurt and only used oat flour. A recipe to keep. Thank you ☺
Hey Djina-I’m happy these worked out with what you had on hand! Always a bonus.
Kate, You might have already answered this questions but I haven’t seen the nutritional info. If you don’t know, at least calorie and fat content. Muffins lot great. I have Granny Smith apples and Vt. Maple Syrup to use up so perfect.
Hi, Ann-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!
Just made these using coconut yogurt because I can’t do the dairy. I used Granny Smith apples. The muffins turned out great. Thank you for such an easy and delicious recipe.
Great! So glad this could fit into your dietary needs, Elia.
I have loved every recipe from you that I have tried. So excited to make these today!
Out of curiosity, why did you dice some of the apples but shred the rest? Is it for added moisture? I’d try changing the recipe myself, but baking is just chemistry experiments that you get to eat at the end, so there’s a reason for everything.
Hey Hannah, I did that for texture and flavor. The little cubs contribute texture and the grated pieces almost disappear, infusing the muffins with apple flavor.
Delicious! Used Bob’s Red Mill gluten free flour and reduced honey to 1/3 cup. Baked at 325F for 20min. Perfect. Will definitely make again!
Thanks, Francine! My GF readers thank you.
Could you please tell me how many carbs are in one muffin if there are 12 to a batch and I use honey. This is for your healthy apple muffins. Thank you.
Hi, Mary. 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!
Wow! These are so delicious. My new favourite go to snack! Can’t wait to try out more of your recipes.
Yes, these are great to grab on the run! Let me know which other recipes you try, okay?