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.
Made these today with my two year old daughter. We had so much fun baking these muffins! We added a tablespoon of chia seeds and baked them in a 24 count mini muffin pan, 325 degree oven for 20 minutes. It turned out perfect. Thank you for the recipe!
I make tons of muffins for my little people and these are by far my favorite that I’ve ever made. Need to make more ASAP!
I made these on a cold rainy Saturday and they turned out great! Been eating them for breakfast and enjoying every bite – love that they’re not too sweet. I made them with honey and sprinkled brown sugar on top.
Really want to try making these but can’t my hands on Apple sauce. Any recommendation for an alternative?
You can make apple sauce really easily. Just peel, core and chop some apples, add to a pot with a little water and cook until soft. Then push it through a seive or whizz in a blender if you want it super smooth
These are OUT OF THIS WORLD! Love your blog <3
What would the nutritional value be for one of these?
It would be really to have on some recipes :D
today was my third time making this :))))) totally loving your recipes! i have a question- my muffins are a bit too wet.. could you advise how i can make it dryer? i use honey is that why?
I’m not sure why that’s the case, CP. Maybe use a little less grated apple, or bake them a little longer?
I also had the same issue of the muffins being too wet. I didn’t use whole wheat as I didn’t have any at home so used regular flour. I also substituted Apple sauce with yogurt since it’s not something readily available where I live. Is it possible that the yogurt was contributing to the wetness? I did bake the muffins a tad longer but not much as it was cooked through. However the texture was very springy and airy. Would you recommend adding more flour to the batter to get the right consistency?
Hi Emily, I don’t understand how the muffins could be too wet, if they are cooked through and springy. They are moist muffins, is that what you mean?
These are great muffins. So moist and deslicous.
I have made these several times – always perfect. thank you!
Just made these gluten free & lactose free! My subs below:
1 cup sweet sorghum flour
3/4 cup tapioca starch
3/4 tsp xantham gum
1/3 cup coconut oil
1/2 cup plain coconut yogurt
1.5 large Honeycutt apples
Came out perfect! Not too sweet, fluffy & delicious!
Hi, Kate. Have you tried this recipe as a cake? I’m looking for a healthy apple cake and wondered if this would work. Thanks!
I haven’t, but I’m fairly confident that will work well! You’ll just need to adjust the baking time. I made a snacking cake out of my [similar] carrot muffins recipe using my 9″ square baker. Baked for about 26 minutes at 425.
I made them again with the red delicious apples but this time used 2 flax eggs and vanilla almond milk instead of yogurt. I used 1/2 teaspoon vanilla. Again, a very delicious muffin!
My 3 1/2 year old daughter and I made these today and they are wonderful! She wanted pink muffins with sprinkles, so we used red galas. When that still wasn’t red enough, I added some food coloring. And then came the star sprinkles instead of the raw sugar topping (same thing, right?) :-) we followed the baking directions for using honey, and they took about 35 minutes to be done, but they were worth the wait! So we have fun, beautiful, healthy, and yummy muffins that the while family loves! Thanks so much!! (I would love to share a pic with you to show how cute these came out, but I can’t seem to figure out how to insert one here.)
Thank you for sharing the recipe! I made these for my one-year-old son and he liked them a lot. I also enjoyed these muffins :)
Hello kate! I’m just wondering if I could make only half of the ingredients?and do I have to adjust the oven temperature and baking time too?thanks in advance!
Hello kate! I’m just wonderning if I could just make half of the recipe?and does the baking temp. and baking time needs to be adjusted too? Thanks in advance!
Did anyone bake this in a Gas Oven? Did it work well? And Did you adjust the temp. lesser? Please let me know. I really wanna try this recipe.
I made the muffins and the taste was wonderful . I baked them for fifteen minutes but they were not a bit gooey inside even though the toothpick came out clean . I baked them for another ten minutes but they did not come out fluffy or completely baked inside while the outside was drying out. Any suggestions? I did try the convection oven.Also I used gluten free flour.
My husband and I are leaving in a few days for vacation at 6am and I was looking for a healthier alternative to airport food, especially at that time of the morning. I made these tonight and they were a huge hit! I always ask my husband to rate any new recipe from 1-10 and he rated it a 10 so it’s a keeper for sure! After both of us eating one, they’re now in the freezer to stay fresh.
The only deviations from the printed recipe I made were the use of organic sprouted spelt flour because that’s what I had on hand and tupelo honey instead of maple syrup. I used granny smith apples which is one of my favorites for cooking. I also put a little oatmeal on the top prior to baking. I did as you suggested and cooked it at 325 for 25 minutes due to the honey and they turned out just perfect and so moist too!
Thanks for this great recipe!
Hi Kate (and of course, Cookie as well)
I made these apple muffins today and they were so delicious! I love all your recipes!
Thanks for sharing!
Tina
Made them this morning with one Granny Smith and one Macintosh. Your recipe is fantastic! The rose so well, made a beautiful crust and were nice and tender inside. Taste was great!
Hi Kate, the recipe looks delicious :) but would oat flour/buckwheat flour be a good substitution to make it gluten free? (will it not make the muffins rise etc.)?
I don’t have any yogurt or sour cream to substitute it! Would they still turn out fine if I didn’t use it, or do you have any other substitutions that would work?
what do you do if you don’t have applesauce?
Bridget, I used milk instead of Greek yogurt.
Chastity, If you don’t have applesauce, add an extra grated apple, or any other purée type fruit you may have. You could mash up some fresh or canned pears, peaches or banana or even pumpkin. Or if you don’t have any of those, a little extra liquid (water or milk or apple juice) may be needed, maybe not. Mix it up without the applesauce and see how it looks. It may be fine without it.
I make muffins a lot, so to mix it up I am baking it (in the oven as we speak) in a round pan so it’s a breakfast cake. (I doubled the recipe so it made two.) I made up an oat topping (oats, flour, sugar, butter, cinnamon), but I used less sugar and butter so it would be a little healthier. Can’t wait to see how it turns out. Although I tweaked the recipe a little so if it doesn’t turn out it’s probably my own fault! :) lol
Thanks for this recipe!
I made this recipe today with the vegan options for my allergic child. I substituted flax eggs for the eggs and soy milk with vinegar for the yogurt. They turned out great! Thanks for the recipe. I just wanted to let you know that those substitutions work like a charm.
These were really good!! Thank you!! These are my new favorites. Can’t wait to try your other recipes
Hi! Can I use half oat flour and half whole wheat flour? Do you think I could add a scoop of protein powder in the dry mix?
These are amazing. I just took them out of the oven and they turned out perfect! best healthy muffin recipe I’ve tried!
This recipe is very versatile. I put it in a 8×8 pan and used 3/4 cup oat flour and 1 cup whole wheat flour. Very, very good! Thank you!!
Hi Kate!
I have these yummy muffins in the oven at the moment! So excited to try them. Would you be able to provide the nutritional facts for these muffins – calories, etc? I didn’t see them by the recipe.
Thanks Kate!
These muffins are fabulous! Best I have ever made. I followed the recipe to a tee and used maple syrup instead of honey. Yum!!! I will be baking them again soon and adding pecans for my nut loving family.
I made these with gluten free all-purpose flour and added 1/4 cup ground flax seed for a more “whole wheat” color. I also used Kiku apples (red, slightly tart) and the flavor is delicious. I’ll definitely make these again and will add other fun ingredients like sliced almonds or chopped walnuts. It’s a keeper!
p.s. I didn’t have applesauce so I used oats soaked in coconut milk.
Thanks, Nett! Glad to hear it!
Greetings from Copenhagen! I was looking for some healthy apple muffins to help go through all the apples on our trees and came across yours. They turned out delicious! I used buttermilk instead of apple sauce and yoghurt and also spelt flour. The mixture of chopped and grated apples really gave the muffins some lovely extra texture. I will def try more of your recopes.
Thank you for sharing it, from a dog loving biking vegetarian across the pond…
Hi Deborah! Thank you for your note. I’m so glad you enjoyed these!
Fantastic! Really moist, and delicious. Nice that they’re so full of healthy goodness.
Thank you, Jen!
So delicious! I made these with regular whole wheat flour, and your vegan substitute suggestions and they were wonderful! Thanks.
Thanks, Olga! Glad to hear it!
Doubled the recipe and added a few oats on top. Taking them on raft trip but couldn’t wait to sample one. Really delicious and bound to be a hit on our breakfast day.
These look amazing! I am dairy free, so do you think that I could replace the yogurt with applesauce and just do 1 cup of applesauce? Thanks!!
Have spent years looking for a good muffin recipe that wasn’t either loaded with fat to keep it light or with less fat that produced a heavy brick.
This is the best muffin recipe I have ever found. Not really sure why it’s so good but it will be my muffin recipe of choice from now on. Thank you so much.
I made these today and everyone loved them, they are really delicious!
Hi. How long do you think the muffins need to cook if I bake them in a mini muffin pan?
Can I use oats instead of flour and normal yoghurt?
Delicious! We used freshly picked McIntosh apples and I only had oatmeal flour on hand. Worked great and a recipe keeper for sure!
This is a fantastic recipe… so moist and flavorful! I just made a batch using coconut yogurt instead of greek, spelt flour instead of all purpose, and swapping 1 of the eggs for a flax egg (1 tbsp ground flax and 3 tbsp water). Also I added a dash each of nutmeg, allspice and cloves. Great with these substitutions!
Hi! This is the perfect recipe to use up my apples and not feel so guilty about it :) I threw my burnt muffin pan can I make it into a 8×8 ? What temp and for how long? Thank u so much
I’ve made these several times (no substitutions, other than I use homemade yogurt)–they’re fantastic! Great for school lunches–my children like to have a “treat” in their lunches, and I like them not to have too much in the way of added sugar, so these make everyone happy.
Thank you very much, Kelly!
Sounds good and I will try this recipe. I would like to see the nutrition value of your recipes since I am cooking for someone who is trying to lose weight.
Thanks
Hi Susan, thank you for your feedback. I am not offering nutrition values yet (I don’t have them yet) but am working on a solution.
I’m sorry to say mine turned out horrible. They were uncooked even though I baked the for more than 15 minutes. Unfortunately this recipe is one that I have failed
Lisa, I’m very sorry they didn’t work out for you. I’m not sure why that would be, unless perhaps you accidentally used the wrong amounts of baking powder/soda?
I made these yesterday for an all day outing with my kids and they were a hit! I used a bit less of the maple syrup (my kids just aren’t used to sweet things), and I subbed almond butter for the applesauce. They were moist and delicious. My kids said they tasted like an apple cake! Thanks!
Thanks, Amyjo! I’m so glad they were a hit!
Hi Kate…ok..here we go…another one of your recipes that I MUST try. Quick question, does it matter if unsweetened or sweetened applesauce is used? I’m sure it doesn’t matter, but wanted to get your input. Thanks!
Made these today with honey and they turned out delicious! Would you happen to have the nutritional information per muffin? Thanks!
I’m so glad! I don’t have nutrition information yet, but I am working on it!