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.

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Trust me, no one will suspect that these fluffy cinnamon apple muffins are healthy! cookieandkate.com

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.

apples

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.

chopped apples

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.

muffin ingredients

How to make healthy apple muffins

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:

  1. Gently stir your flour to loosen any clumps.
  2. 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.
  3. 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.

muffin batter

Healthy apple muffins batter

Healthy apple muffins before baking

Best healthy apple muffins made with maple syrup and whole wheat flour! cookieandkate.com

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Simple, healthy apple muffins recipe (no crazy ingredients!) - cookieandkate.com

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Healthy Apple Muffins

  • Author: Cookie and Kate
  • Prep Time: 15 mins
  • Cook Time: 13 mins
  • Total Time: 28 minutes
  • Yield: 12 muffins

5 Stars 4 Stars 3 Stars 2 Stars 1 Star 4.8 from 688 reviews

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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

  1. 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).
  2. 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.
  3. 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.)
  4. 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.
  5. 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.

Kate and Cookie

HELLO, MY NAME IS

Kathryne Taylor

I'm a vegetable enthusiast, dog lover, mother and bestselling cookbook author. I've been sharing recipes here since 2010, and I'm always cooking something new in my Kansas City kitchen. Cook with me!

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Comments

  1. Abbie N

    Delicious !!! Best Apple Muffins I have ever tasted. I had to sub whole buttermilk for
    Greek yogurt and I used an extra large Envy apple. I added some apple pie spice and nutmeg just because I had some leftover from another project. the are so moist yet light and fluffy. Plus the raw sugar on top gives them a delightful crunch! I filled 12 standard size muffin cups all the way to the top then baked at 425 degrees for 5 minutes then lowered the oven temperature to 350 and baked for another 15 minutes. i will definitely make this my go-to Apple Muffin recipe. Thanks Kate!

  2. Tessa

    Wow. What a great recipe! Thanks so much for creating a great tasting and beautiful muffin. They are light and fluffy and packed with apple flavor.

    I made these today on a very cold and snowy day. They made us very happy.

  3. Heidi

    How could I add oatmeal to these to make even healthier?

    1. MCM

      You can use ground oats instead of wheat with a 1:1 substitution. It turns out great! I grind my own (in a coffee/spice grinder). Or sometimes I buy oat flour already ground from the supermarket)

      1. Geoff Turnbull

        Hi Kate, is shop bought oat flour also 1:1 ratio? Also, is blitzing rolled oats just the same as bought oat flour?
        Cheers
        Geoff

        1. Cookie and Kate

          Hi Geoff, I have all the instructions on how to make your own oat flour and how to substitute it in this post. I hope this helps!

  4. Ellie

    These are really good!
    My hubby and I are trying to cut out refined sugars so it was nice to find a recipe using maple syrup and the natural sweetness of apples ! Definitely would make again

  5. Stephanie W.

    Delicious! I love them so much amd my husband too. I can’t wait to make them for my friends and family. I made them gluten free and dairy free. I used mixed berry yogurt because that is all I had.

  6. Kristina

    These muffins are delicious! I was searching for a healthier recipe with whole wheat flour and found it here. I’ve made many muffin recipes and weren’t really pleased with the taste. It looks like granny smith apples in the picture – I only had Evercrisp and they turned out great! I added a homemade-crumble topping too. Thanks for this recipe :-)

  7. Tania

    Hi Kate
    If making apple muffins and I don’t have applesauce, what can I substitute?
    Cheers
    Tania

    1. Rolande baker

      I also wanted to know so googled it; In baking, applesauce can be substituted with a variety of ingredients, including mashed bananas, pureed fruits like peaches or prunes, and even yogurt or sour cream. Mashed bananas are a popular choice due to their similar texture and moisture content, while fruit purees offer a range of flavors. In some cases, you can also substitute oil or butter with applesauce in a 1:1 ratio. Hope it helps.

    2. Dan

      This recipe calls for grated apples. Just use the smaller holes on the grater and you get applesauce :)

      1. Tania

        Thank you!

  8. Angela

    So good!

  9. Rina

    I followed this exact recipe to a tee and also made the homemade apple sauce you mentioned in a comment. I had an abundance of apples that I needed to utilise and wow I absolutely love it. Contemplating whether I want to share or just keep to myself haha. Thank you!
    Going to look at the other recipes you have to offer on your site the next time I want to tap into my cooking/baking mood.

    1. Cookie and Kate

      Hi Rina, I’m so glad you enjoyed it! If you like these muffins, the banana and blueberry muffins are also favorites.

  10. Dima

    Thank you for sharing your recipe. It looks delicious. I want to make it today, but I only have applesauce. I don’t have apples at home right now.
    Is it possible that I can still make it!?
    Thank you
    Dima – New Zealand

    1. Cookie and Kate

      Hi Dima, I recommend it as written.

  11. Nicole

    Husband is looking for a cinnamon muffin recipe (no apples/fruit). How can I modify this recipe?

    1. Cookie and Kate

      Hi Nicole, I’d suggest finding a different recipe developed as a cinnamon muffin. The two cups of apples add flavor, moisture, and texture to this recipe.

      1. Abi

        Love this!

        Do you use cooking apples (like Bramley apples) or regular apples?

        1. Cookie and Kate

          Hi Abi, I tend to use Granny Smith green apples, but you can experiment with your favorite varieties for baking.

  12. Liliana Groh

    Honestly so delicious I had to stop myself at 2 plus kids leftover. I added crumb topping on half but it tasted better without it. I had regular cae sugar for the top and that was really good.i also used whole oatmeal 1 cup and whole wheat flour 1 cup.

    1. Rachel

      Hi could I just use regular white all purpose flour?

      1. Cookie and Kate

        Hi Rachel, yes you can use all purpose flour.

  13. Emily

    It’s not uncommon for me to end up eating three of a baked good the day I bake it and then regretting it the next day. My regret this time was not because I felt bad physically after three goodies — three of these wholesome muffins left no such sugar hangover. Instead, it was because they taste even better the next day, so I wish I’d saved more.

    I am glad that I made a double batch. These will be great in lunchboxes. The kids love them, and I feel good about feeding them to them.

  14. Mary Anne Kennedy

    What’s the difference in taste if I use canola oil instead of extra virgin olive
    Oil?

    1. Cookie and Kate

      Hi Mary Anne, canola oil has a more neutral flavor than olive oil, which can have different flavor profiles that are fruity and robust or even peppery, depending on factors such as variety of olives it is made from or the region of origin.

  15. Robin

    Thank you for this wonderful recipe! The muffins turned out moist and not too sweet. The only thing I modified was I did a combo of whole wheat flour and all-purpose flour (1C whole wheat, 3/4C all purpose). My hubby isn’t big on everything I make being “whole wheat” ( you know how guys can get) so I osometimes do a combo of flours when I bake. Tasted like a bakery muffin!

    1. Lulu

      You mean he’s complaining about home-baked muffins he’s getting? Just go ahead and make them the way YOU like ‘em—if he doesn’t like it, he doesn’t have to eat them! I can’t really tell the difference when I use whole wheat pastry flour.

  16. Diane McKay

    I made these muffins which were a little time consuming but well worth it. Love the healthy ingredients to the mix.

  17. Laura

    Has anyone made this as a cake (maybe in a Bundt pan) rather than muffins?

  18. Heno

    Finally a recipe without sugar and butter that tastes great! I didn’t have all ingredients so I replaced apple sauce with equal parts smushed bananas and left out vanilla extract but it came out great! I also added poppy seeds and walnuts.

  19. Lynn M

    These are absolutely delicious! (So are the blueberry, banana, and pumpkin.) Can they be baked in a standard loaf pan? Time?

    1. Cookie and Kate

      Hi Lynn, most loaf breads take about 55 minutes in a 9×5 pan, you might check it with a toothpick a little earlier to test it for doneness.

  20. Denise Ing

    These are delicious. I had lots of Granny smiths to use up. It was perfect for using up the apple sauce, and yogurt in the fridge. I didn’t quite have enough yogurt so I used sour cream as well. Delicious. I also used less maple syrup and the were delicious.

  21. Maya

    This is a fantastic recipe, thank you! I make it without any added sugar/maple syrup (I know it’s a matter of taste and habit, but I eat very little sugar so when I first made this recipe with 1/4 cup maple syrup I found that even that was a little too sweet for me) and I do 1 cup gluten free flour and 3/4 cup almond flour and it works brilliantly. We all love it, including my 1 year old. :) thank you for this recipe!

  22. Alyssa Cooke

    Can you freeze these well?

    1. Cookie and Kate

      Hi Alyssa, yes these freeze well. Just defrost them in the microwave.

  23. Eli

    Can I use this recipe to make apple bread (so, in a loaf rather than muffin pan)?

    1. Cookie and Kate

      Hi Eli, yes, that should work but will need a longer baking time. I would start checking with a toothpick at 45 minutes, and pull it out when the toothpick comes out clean.

  24. Debbie

    These were delicious. I only had strawberry applesauce on hand and I think it gave a touch of additional flavor. I used coconut sugar to sprinkle on top. Thanks!

  25. sarah brown

    please explain “see “buttermilk” above. I have read this recipe twice from the top and haven’t seen “buttermilk”.

    1. Cookie and Kate

      Hi Sarah, that detail is included in the section on how to make the recipe dairy free — you would follow the same instructions as above to sub vegan buttermilk for the yogurt in the standard version of the recipe.

  26. Carrie S

    I made an interesting mistake, accidentally adding garam masala instead of cinnamon. They were on the border between sweet and savory. The heat was divine!
    The apples I used were right off my tree, a little early so very tart.

    1. Cookie and Kate

      Hi Carrie, I’m glad it still worked out for you with the unexpected spice! That seems like a happy accident and an interesting flavor profile. Thank you for sharing.

  27. Sarah

    I only had extra virgin olive oil so I used it as that is what the recipe said…but now the muffins taste like olive oil?

    1. Cookie and Kate

      Hi Sarah, some olive oils are more flavorful than others. Many people enjoy the flavor profile. You may prefer a neutral oil in the future, like avocado oil.

  28. Ann

    These muffins have a lot of flavor. I ran out of my white ww four and just used 3/4 cup of king author AP. Also 1/2 olive oil 1/2 coconut oil for the oil. The biggest chore is grating and chopping. I used wild apples my hubs picked today. Results are really good. Thx for the recipe! Yum!

  29. Carol B

    I made the recipe as directed. I did add pumpkin pie spice 1/2 teaspoon in addition to the cinnamon. Easy and very apple yummy! Thank you for making it healthy too.

  30. Barbara A Desjardins

    Today, I made the recipe with King Arthur gluten free 1:1. and I added dried sweetened cranberries with the apples and no other changes.
    These muffins were the BEST!
    Thank you for this recipe!

  31. Heather

    Good apple flavor, but I think next time I’m going to grate all the apples because my kids weren’t a fan of the chunks. I added 1/4 tsp nutmeg, and it still didn’t have enough spices in my opinion. Next time I will add more cinnamon and extra nutmeg. I used AP flour, but subbed out 1/4 cup oat bran.

    1. Cookie and Kate

      Hi Heather, thank you for sharing!

  32. Nikki

    Holy smokes! I was blown away by these muffins. I used regular flour since that’s all I had and didn’t change anything else. For the 1/2 cup of syrup or honey, I filled up my 1/2 cup scoop about 3/4 of the way with maple syrup and topped off the rest with honey, so I didn’t adjust the cooking temp per the instructions when using honey (since I wasn’t using a lot). I used some mealy red apples I was going to compost and the result was still spectacular. I have never eaten such a moist muffin. I sprinkled the top of muffins with some rolled oats before sprinkling the sugar on top to make them prettier and give them a little more texture. Amazing! TY Kate!

    1. Cookie and Kate

      Hi Nikki, I’m so glad this recipe worked for you, especially to use up apples that were subpar. Thanks for taking the time to rate and review the recipe.

  33. Andrea J

    These are so good that I just made them for a 2nd time this week! I love that they are healthy & made with whole wheat flour. I followed the recipe as written, but I did add 1/2 cup of chopped walnuts. I’ll be trying your banana ones next!

  34. Danielle

    Do you leave the skins intact on the apples? In the pictures it looks like the skins are on, but the grated apples look like they are peeled? Thanks.

    1. Cookie and Kate

      Hi Danielle, I leave the skin on in both the diced and grated apples.

  35. Mary

    Awesome! I used apples from our backyard tree and used organic coconut sugar for the topping. Delicious!!! Thank you Kate:)

  36. Allison

    Is the temp correct to be 425 all the baking time, or similar to your pumpkin recipe where is is 5m then lowered to 350?
    Love your recipes!

    1. Cookie and Kate

      Hi Allison, I recommend the recipe as written!

  37. Trista

    Wonderful recipe!! They turned out a little underdone on the bottoms/center even though my toothpick came out dry, I think I need to lower my oven temp for the second half of cooking, because the tops of the muffins were browned. But other than that the flavour was so so wonderful. I added a dash of nutmeg as well for fun and it was perfect. I WILL be making these again. It’s always good to have a guilt-free nutritious snack in the house. Thank you Kate <3.

  38. Divya

    This is one of the best muffin recipes I’ve ever tried! Used half the measure of honey and it still came out so perfect. Moist and delicious! Thank you Kate!

  39. Julie

    These are quite possibly the best muffins I’ve ever made. The texture of the apple was perfect and the flavor was very pronounced thanks to the grated apple as well as the applesauce. Thank you for making a muffin that isn’t loaded with sugar! I’d happily give these to my family for breakfast without guilt.

  40. Tessa

    I have been looking to add some variety to my tried and true muffin recipes; this will be a new staple! Moist and Delicious. I will add more cinnamon next time (personal preference) teenager approved.

  41. Carol

    Can I substitute butter in place of the oil. They do look and sound delicious.

    1. Cookie and Kate

      Hi Carol, using butter would require adjusting the liquid ingredients slightly and would result in a dryer muffin. I don’t recommend it.

  42. Karen

    Hi can I swap spelt flour for whole wheat flour?

    1. Cookie and Kate

      Hi Karen, you could, but you would need to adjust the liquid because spelt absorbs less liquid than whole wheat flour. It would take some testing to get the proportions right.

  43. Marlen Paniara

    This looks so good! Can I use stevia instead of honey/maple sirup?

    1. Cookie and Kate

      Hi Marlen, yes you can, but it will impact the flavor.

      1. Marlen Paniara

        Thank you. i will definitively try it!

  44. Mary Abbott

    I made this recipe exactly as written and it was delicious! Next time I will add walnuts because I like a crunch. I will save this recipe to my favorites! Now I am excited to try your other “healthy” muffin recipes. Thanks for sharing this yummy, healthy recipe.