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
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.
If you love this recipe: You will also love my zucchini muffins, carrot muffins and banana muffins! Here are more apple recipes for you, too.
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.
Hello Kate (and Cookie),
I first located your information for “best steel cut oatmeal” online (I forgot the ratio of oats to water). Then I tried your recipe with milk and roasting the oats before cooking Wow! It was great! Thank you. I added dried cranberries and roasted pecan pieces before serving. Fantastic.
Because of this experience, I went back online to look for an apple muffin recipe and found your “healthy apple muffins” and have made them several times since. To make a more complex flavor, I add 1/2 C fresh frozen cranberries quartered or halved that I sprinkle with 1 t of Stevia or Zero Carb Granulated Erythritol “sugar” and let rest for 15 minutes, 1/2 C roasted walnuts, I use an egg substitute, and sprinkle in about 4 – 5 T of Hemp Hearts for extra protein. It’s fabulous! And I can’t wait to bake your healthy carrot muffins and pumpkin muffins.
I want to thank you so much for putting out such wonderful recipes and will most likely order a copy of your cookbook.
Made these for the toddlers breakfast. Threw in a dash of extra salt, cinnamo, nutmeg and vanilla (really just a dash!) before baking. I didn’t *quite* have enough honey. They smelled great baking, but tasted like flour more than anything. Will try again with the maple syrup and more than just a splash extra of some ingredients.
Thank you for the recipe, it is absolutely delicious! I topped with brown sugar since I didn’t have raw sugar and it was so good! Very happy!
That’s great to hear, Sarah!
Hi! I would love try to try your recipe. Can I had add oats to it? If so, how much?
Thanks!
Hi Angie, I tested adding oats in my Strawberry Oat Muffins and have guidance for you in there!
These are amazing! My daughter has them in her morning tea for school everyday!
I use a pumpkin spice in them instead of just the cinnamon.
Thank you for your review, Bec!
This was my second or third time making these delicious muffins. Easy to make, bake and wonderful to eat. I just add another teaspoon of cinnamon…a favourite ….and more on top instead of the sugar. These also work for my husband who has to be careful about sugar intake.
thanks for a great recipe.
You’re welcome, Shelley!
Hi Kate, these were really amazing muffins and so easy to make and freeze too. They were just the right sweetness and softness. BTW, I used monk fruit to sweeten and added some mashed banana too. Thank you! I am going to try your carrot ones next. :-)
Some of the best muffins I’ve made in a long time. I subbed the honey for brown sugar and I added fresh ground green cardamom. Added such a great flavor with the apple!
These were delicious! I replaced the flour with 1.5 cups oat flour and 1/3 cup almond flour. They were a touch on the dry side so I may pull back slightly on the oat flour. I also sprinkled a little oat flour and coconut sugar mixture on the top. They were for my kids and I knew the added sweetness would be a treat for them. So glad I found your recipe! Now it’s really starting to feel like fall!
Should I peel the apples before?
No need to peel the apples.
Hi! I don’t have Apple sauce on hand, can I replace it with something else? More yogurt? A banana?
This is best as written. I haven’t tried it with something else, sorry!
I just made these and they are delicious! I didn’t have applesauce so I just used another 1/2 cup of grated apples and didn’t drain them. I ended up with enough batter for 15 muffins. They are seriously so yummy!
Great to hear, Nicole!
Just made a triple batch using some fresh fall apples. My only regret is that I didn’t make more! These are going in the freezer for easy, nutrient dense breakfasts this school year. Followed recipe as written using honey. Reduced the cooking time as instructed and they came out beautiful.
That’s great to hear, Jessica!
So delicous! I did honey and added some walnuts and nutmeg to mine :)
I made these with a few modifications. Very yummy!
First I added 1 scoop of unflavored protein powder. I will try 2 next time.
Used buttermilk instead of Greek Yogurt
Cooked my apples a bit before placing in batter
Added 1/2 cup oatmeal
1/2 cup of walnuts.
I did turn down the heat and baked them longer but not sure how much longer. Just kept testing them.
Used the free APP Recipe Calculator to check my numbers and it’s great.
I love this recipe! I make these all the time. i leave some of my apple pieces a little bigger so i get a few chunks of apple in the muffin. Everybody loves them and it’s hard to convince them that they are healthy!!! It’s a total win!
I baked these today for the first time, using apples my kids and I picked at the farm this weekend. WOW! They are absolutely delicious. Moist, just the right amount of sweetness, and a nice mid-level crunch to the apples (not crunchy and not mushy). Thanks for the recipe!
Very good versatile recipe! Great for those apples when they’re petering out. Easy to sub out things…like once I didn’t have apple sauce so I used pumpkin puree…or I didn’t have yogurt so I used milk(alternative because I am dairy free for my breastfed baby currently). They always come out great! This recipe is a keeper!
I think I’m in love! These are truly fantastic – light, moist, and FULL of apple flavor. I know what I’m talking about because my friends used to call me “the muffin lady” due to the number and variety of muffins I make. These are one of the very best recipes I’ve tried.
Can I use this recipe for 48 mini muffins? How long should I cook them?
You can try it! You will want to reduce the baking to half, but be sure to keep an eye on it.
I have made this recipe multiple times. I make at least two dozen since I share with friends and relatives. Everyone has given positive feedback and they usually ask me for the recipe.
This is a 5 star winner!
Great to hear, Gila!
These are excellent and brought a big smile to a two year old’s face. Made as written, EVOO, and Granny Smith.
Sounds perfect, Jack! Thank you for your review.
This recipe is AMAZING! I saved the pissed juice from the grated apple and added it to the wet. I used gluten free flour. Half maple and half honey. I tossed in some pumpkin pie dressing, and topped with brown sugar. I used a mini muffin tray and preheated to 450, but dropped it to 350 at bake time. Cooked for 15m and left in muffin tin for 20m to rest.
Fingers crossed the kid loves them. My whole house smells like Cinnamon Toast Crunch and I’m in LOVE!
Might try adding flax seed and swapping in a bit of almond flour next time.
Thank you again!
You’re welcome, Jacqueline!
Can I substitute spelt flour at the exact same amount?
I believe that works in my banana bread recipe. I haven’t tried it here though. Let me know if it works for you!
Hi Kate, thanks for all the great recipes. I make your banana bread almost every week for my family. It’s a big hit!
My 6 year old is really into apples right now and asked for these muffins. Is there a way to convert them from muffins into a bread loaf? That way I can fit a double batch of them into my air fryer. :)
Can you use this recipe for mini muffins?
Hi Donna! It should be ok. Be sure to cut the bake time in half and keep an eye on it.
Hi Kate! Love you and all your amazing recipes!
What variety of apples do you recommend for these muffins?
I prefer a green apple, but you can use the apple of your choosing.
Do you think switching the apple pieces with shredded apples will cause any issues? My kids don’t like pieces of fruit in their muffins so I’m thinking making this modification.
I recommend this best as is. But, you could try it. Let me know how it turns out for you!
Just made a batch of your “Healthy Apple Muffins” and they’re totally delicious! I start off all my muffin searches with “healthy” and was thrilled with all the ingredients in yours! I often have to replace the ones I find that have sugar or “bad” oils with maple syrup, “healthy” fats, and (organic) whole wheat flour, but I didn’t have to change anything with this one! I make a batch of muffins every week, often with bananas and/or blueberries, but this one will definitely make the rotation more often! Can’t wait to try more of your recipes! Thank you!
Hi applesauce it’s not readily available in my country. It’s at some health shops but in tiny tiny jars because it’s only used for topping meats here.
Is it just boiled and mashed apples? I’d not could you give me some basic guidance on how to make it before hand? Thank you
Hi! Here is my How to Make Applesauce recipe as a reference.
Hi Kate,
I didn’t have applesauce so I added in a little extra Greek yogurt and one more cup of chopped apples. And a quarter teaspoon of nutmeg. They are moist and delicious! Highly recommend with apples in season right now, I used honeycrisp:) ( it’s five stars but not letting me click on it. )
These look delicious, i definitely want to make them. I don’t have Greek yogurt or buttermilk on hand, can I use any non dairy milk? Or does it need to be thick? Can’t wait to try the pumpkin ones also!
This is best as written. Follow my How to Make Buttermilk recipe for help on making buttermilk!
I am new to baking; I don’t generally have the patience for it, but these muffins were quite easy to put together and came out SO SO GOOD! I have been looking for recipes to make for my 1-year old twins and I love that these are sweetened with maple syrup and use greek yogurt (I buy huge tubs and need to find uses for it). I did one egg and one flax egg for the added benefits. I also only used grated apple (honeycrisp), no diced, to keep the texture less chunky for them. They came out super moist, a little spongy, and the perfect level of sweetness. Amazing and will definitely be in the autumn rotation!
Great recipe with plenty of room for creativity! However I would have to disagree with the healthy part! Maple syrup is very sugary!
This recipe is absolutely delicious! I’m always looking for healthy stuff to eat!
My friend and I hike every Sunday morning. She brings coffee and I bring muffins. My sister gave me a whole bunch of apples from her farm so this was perfect! It used up some of my supply and I already had made some applesauce! Thank you for sharing!
You’re welcome, Carol!
These are so good and moist! I also added pecans to mine, yum!
I made these recently and was so pleased. They were excellent. I love that your recipes that are healthier and taste so great!
That’s great to hear, Dianne! Thank you for your review.