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.
SO much easier to weight ingredients. Can you include weights on your recipes?
Hi Sue! I appreciate your feedback. I try to provide weights when I can.
Kate! These are delicious! I just made a double batch and they are not going to last long. Thanks for this recipe, it’s already a favorite!
Applesause – this and several other recipes call for “applesauce”. Is this applesause with sugar or no sugar kind?
Hi! I think apples are sweet enough, mine was unsweetened. I have a homemade version on the blog!
Perfect as is! Thank you!
Can whole wheat pastry flour be subbed for your recommended flours?
Hi! Sure, you will likely get a fluffier result. Let me know what you think about it!
I absolutely love this recipe!! I didn’t have a ton of yogurt left so I combined the leftover with buttermilk with turned out fine. I also used golden delicious for the cubes which gave it a nice crunch and red delicious for grating. I also reduced on the amount of maple syrup and it turned out great! Also for the spices, I added nutmeg, allspice, and ginger with the cinnamon which really brought out the “fall” flavored!
Turned out great! Used maple syrup, homemade yogurt, coconut oil, fresh apples from the orchard.Great recipe. For the juice from the apples gained by grating the apples save to drink later..yum!!
Thanks for another amazing muffin recipe! These turned out great! I used sour cream for the yogurt and I got 14 muffins. The whole house smelled incredible and they were so light and fluffy. <3
I made these exactly as written (other than no turbinado sugar on top). They came together easily. When I ate my first muffin, I wasn’t sure I liked them. I used maple syrup as the sweetener and my initial reaction was that they weren’t sweet enough. It took a few minutes, but they actual grew on me. They are just sweet enough. I will definitely make again.
Another amazing recipe that has now become a go to!! I followed this exactly per the directions and the muffins were so delicious! I used a combo of 2 red apples and two green apples. I also used unbleached regular flour as I didn’t have any whole wheat flour available. Thank you for your wonderful recipes as your site is my go to for vegetarian dishes that my husband will actually eat!
Wonderful to hear, Colby! Thanks so much for reporting back.
Very good! I used 1C wheat and the rest white flour. About half and half on the honey and maple syrup. Subbed homemade low sugar apple butter for the apple sauce and it added great flavor. The sugar crunch on top was perfect!
Hi what kind of apples do you recommend best for these muffins? I can’t find that info in the summary above the recipe or elsewhere. Sorry if I overlooked it. Thanks!
Hi Vee! I believe I commented already, but wanted to make sure you got your answer. I used granny smith, but you can use what you like!
I made these muffins yesterday with our haul from our local orchard and they were delicious! I will definitely be making them again.
Hi what kind of apples do you recommend? Thanks!
Hi Vee! I used granny smith for these, but you can use your favorite!
Thank you! Can’t wait to make them!
Made these this past weekend. Used local honey for the sweetener. They were amazing. My 15 year old son couldn’t stop eating them and ate 5! Guess thats the best compliment. A crumble topping would make them extra fancy.
I tried this recipe. They are a hit! What I like best is that this a very hearty muffin. I have one for breakfast and I don’t get my 9:30 am cravings. I am trying your banana muffin recipe next. Your recipes make it easy to add more plant-based protiens into my diet. I don’t have to join a program, I can just follow YOU!
Good basic recipe, but unfortunately had no flavor! Even added extra cinnamon (I always do) but we all agreed they were pretty plain– tasted more like a baked pancake with apple chunks. Tasted good warmed up with butter and extra cinnamon on top, and would be great with peanut butter or jam!
Perfection in a muffin! Tender, flavorful and healthy. I used half coconut oil and half grape seed oil and half whole wheat flour, half oat bran and am swooning. Delicious fall recipe! I also sprinkled the top of each muffin with chopped walnuts before baking. Make these and show yourself and your family what love tastes like!
I havent made these yet (going to soon!) and I dont leave comments often but I just have to say THANK YOU so much for making simple, healthy recipes using easy to access ingredients and giving extremely useful bits of knowledge on how to make them. I recently ran into a recipe for sweet potato muffins and I wanted to cry by the end of making them it was so complicated and ridiculous. So thank you so much from a very amateur baker.
Would this be just as good in a load pan??
Hi Amanda! I haven’t tried it, but I believe others have and didn’t mind the result. If you try it, you will need to bake longer. I’m not sure the exact timing.
Easy and worked the first time. Very moist with lots of Apple flavor. Would definitely make again.
These were so easy to make and delicious. Everyone who ate one basically took a bite, looked up, and exclaimed how tasty it was.
Awesome thanks so much couldn’t wait to try them Delicious thank you
I made these with my 3 year old son, using apples from apple picking last weekend. I didn’t have any yogurt on hand so we subbed in vegan buttermilk. They came out perfectly and are so delicious! Not too sweet, moist, and picky eater approved :)
Wonderful! What a fun activity and way to use your apples. Thank you for sharing, Kelly!
Hi Kate! Excellent muffins I just made during a conference call ;-). I would like to make them again tomorrow but with a mini muffin pan. How long should I cook them for? and I will be using honey instead of maple syrup. Thank you! Ps. and for Ms. Fitzgerald.
Hi Gina! You can make them as the same, just shorten the bake time by half and keep an eye on them as they will be done sooner. Enjoy!
Thank you!
I made these with Rome apples and they were delicious. I think next time I might add some walnuts, will definitely make them again!
Can you replace greek yogurt with coconut yogurt? I can’t have dairy :/
Hi Kaya! See my vegan notes for alternatives. I hope you can enjoy them! It’s below the recipe instructions.
Made these last week with Cortland and Spartan apples and IT WAS AMAZING! Your recipes never disappoint! I had a huge bag of hand picked apples but no apple sauce so I added in an additional 1/2 cup of grated apple and a bit more yogourt. The texture was perfect but next time I’ll definitely try it with applesauce.
Thank you! I appreciate your review.
I going to try with frozen apples
Just made these this morning – they are super delicious! Thank you for the recipe!
I made mine with asian pears instead of apples, all applesuace (as I was out of yogurt) and added a handful of crystallized ginger – super fun!
So good, we make these weekly now!! Thank you!
These are scrumptious and just the best muffins! I was shocked how amazing they were, truly a wow, stand out muffin. I used applesauce instead of Greek yogurt and they were great! Also used honeycrisp apples instead of Granny Smith, they were like eating mini apple pies but healthy and not full of sugar. Pure goodness.
Thank you for letting me know, Kate! I appreciate your review.
I made these today & they are fabulous!! Will be a new favourite in our house!
Living in Zimbabwe we can’t get fancy ingredients so it’s great to find recipes that I have everything in my pantry/fridge
Thank you so much
Thank you for sharing, Kirsten!
I lost a few pieces of my finger grating the apples as recommended. I don’t know that apples are meant to be grated.
Oh no! You need to be careful anytime you use a kitchen tool. I’m sorry to hear that.
I made this twice: with 1/2 oatmeal flour and 1/2 Bob’s Red Mill Gluten-free flour for the gluten-free version, and King Arthur’s White Whole Wheat Flour. The muffins were delicious, very moist and flavorful. They domed nicely in the oven but deflated to a flat top after they cooled down.
Hi Shinta, It may have bee your combination of flours. But, I’m glad you were still able to enjoy them.
These are so delicious!! They are super flavorful without being very sweet which is just perfect for me.
Thank you for your review, Char!
Hello, I tried the recipe and thee muffins came out delicious! Well I did change some things…., I used 1 cup of Greek yogurt instead of 1/2 cup of applesauce and 1/2 cup of Greek yogurt. I used olive oil. I didn’t have eggs and used 2 “flax eggs” as you suggested. And I put in some oats as well instead of making all whole wheat…but they were perfect! My hubby loved them.
Where do I post the pics?
Hi Rebecca! Thank you for sharing. I’m happy you love them. You can always share your pictures on social and tag Cookie and Kate!
Best apple muffins I’ve ever had. I made mine vegan and used organic all purpose white flour, buttermilk from the suggestion above, and more applesauce rather than flax eggs. They came out great. Thank you!! I do apple sauce for the banana muffins as well, always a huge hit.
Hooray! I love it. Thank you for sharing, Liv.
These were the most delicious muffins I have ever made! I used up some old gala apples that I need to find a use for, as well as I added just a small amount of nutmeg along with my cinnamon. I didn’t have any sugar to put on the top but they were terrific. Love your recipes Kate!!
I’m glad you loved this one and other recipes, Janice! I appreciate your review.
Do you think it would turn out okay if I replace the chopped apple with more shredded apple? I don’t think my kids would like the apple chunks.
It may be ok, although the texture of your muffin may be slightly different. Let me know!
Loved these! Great apple taste – used a snow sweet and a ashmead’s kernal, plus homemade applesauce from a variety of apples picked from an orchard south of us and yogurt from the creamery a few miles from the orchard (Cabot). Used local maple syrup (thank goodness we live in Vermont) and King Arthur Flour. These muffins were an absolute treat with full flavor – probably because of the very generous amount of apples and the double cutting sizes (diced & grated). Did add 1/2 t. nutmeg. Great also served with a bit of seriously sharp Cabot Cheese.
MOST delicious muffin ever! Making my second batch now. I added walnuts on top that got nice and toasty. Truly delicious. Many thanks for the recipe!!
You’re welcome, Jill!
Me and my daughter did it last night! Soo good.
Another winner! Love your banana bread and pumpkin bread recipes so trying this one was a no brained. SUPER strong apple flavor, in a good way! Thank you!
Super good, even the first time I tried this recipe! I used Granny Smith apples.
I’m glad it was such a hit, Lina!
I made this recipe and the only thing I did differently was use tapioca flour which I could with a lot. The tops cooked a nice golden brown but the center is chewy and a bit tough. Any ideas?
Hi Dorothy, Unfortunately, it was likely the tapioca flour. Sorry I can’t be more help!
Can I replace the oil with butter
Hi Yolande, I haven’t tried it so wouldn’t be able to say for sure. Sorry!
Delicious muffins. Made them twice with no changes to the original recipe and they are wonderful and moist. Best apple muffin recipe ever!
Happy to hear that, Ani! Thank you for your review.
Hi Kate (and Cookie!), My aunty Ann B. gave me your cookbook two holiday seasons ago, and I have made almost every recipe in it. Now, you are the top hit whenever I search online for new things to cook. Ann and I are the family vegetarians, pretty much life-long, and good friends. I love that we share your love of healthy food. Muffins are in the oven, and smell delicious. Thanks for all you do! Ginna
I love that you have made every recipe! Thank you for sharing.
Light, moist and very delicious. Thanks for this great recipe.