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.
Hi there, I added nutmeg, molasses instead of honey and apple extract. Family said it was a winner. Thank you.
I made these for a grab-and-go breakfast during a race weekend. Two muffins, three mornings in a row, where exactly what I need to start my super early days. The flavor was excellent and the texture was perfect. I can’t wait to make again and enjoy them on slower-paced mornings with some coffee. Thank you!
SO good! I used maple syrup, grapeseed oil and topped them with some coconut sugar and cinnamon. Baked I think about 15 mins. My kids loved them, and the one who would usually refuse to touch anything someone else has touched actually ASKED to eat the remainder of her little sister’s muffin. Definitely will make a double batch next time!
SO good! I used maple syrup, grapeseed oil and topped them with some coconut sugar and cinnamon. Baked I think about 15 mins. My kids loved them, and the one who would usually refuse to touch anything someone else has touched actually ASKED to eat the remainder of her little sister’s muffin. Definitely will make a double batch next time! Mine made about 18 muffins.
Thank you for sharing, Erica! I’m glad they were such a hit.
Can I make these in a mini muffin tin? Would timing in the oven change do you know? Thank you!
Hi! Yes, that should work. Usually it is just half the time at the same temperature. Keep your eye on them and adjust the time as necessary.
I didn’t have applesauce, so I used mashed banana, and they cane out great!
I’ve made these many times almost exactly as written to take to work as a healthy snack. I don’t have the right flour so usually just mix a small amount (1/4 or 1/2) cup of white and the rest whole wheat. Use whatever apples I have around and bake at 425 for 13 mins in silicon muffin cups (they’re small so i get around 17 muffins) . I’ve sometimes added in frozen blueberries.
I have frozen unbaked batter in the silicone cups and then bake them at the same listed temp but for a bit longer (just check around 15 min and use a tester) – they’re always great.
It turned out great! I didn’t have any applesauce, so I doubled the recipe with yogurt. Used the maple syrup with coconut oil & topped it off with brown sugar. I’ll definitely make it again, and I am going to try your other recipes.
Today I made the muffins for the first time and they came out perfectly, soft and tasty.
I liked the very detailed instructions so no mistakes.
Thank you for a great recipe!
Can you substitute the applesauce with something else? I don’t have applesauce! :(
Hi Vanessa! Based on my similar muffin recipes, I think you could replace the applesauce with additional Greek yogurt (use the same amount). The muffins won’t taste quit as apple-y, but they’ll still be great!
Could I do the same thing but vice versa (replacing the yogurt with applesauce)?
Thanks
I think so!
Hi! I am eager to make this but I only have white all purpose flour and with these times I am finding it difficult to find the right flour. I know it substantially lowers the healthiness of the muffins but do I just substitute 1:1 white all purpose flour? TIA!
Hi Mabel! That should work fine. I hope you like them!
Thank you so much for your prompt reply! I can’t wait to try them. :)
tried this recipe the other day and the muffins were AMAZING! even my picky-eater partner loved them, as did my toddler.
These apple muffins are the best! We love them. Can’t wait to try some of your other recipes. Love the nutrition factors as well. Thanks!
Just made this recipe…and LOVE it!
I used an extra 1/2 cup of yogurt instead of applesauce.
They turned out beautifully. Thank you so much!
These were amazing! So fresh and moist I will not eat another muffin not homemade agin. Loving your recipes! They always turn out great, delicious and easy.
These turned out perfect! The Greek yogurt I had on hand was Liberte 3.5% fat, reduced sugar vanilla flavoured, which obviously worked well. I will definitely be making these again!
Can you use parchment paper muffin cups instead of untreated pan?
Sure! That may work. You may want to coat the cups, depending on your experience, as they may still stick to the paper.
I’ve made these twice and have received very good reviews. I make the applesauce by cooking a chopped apple in the microwave. Both times I have added crumbled walnuts to the top before putting them in the oven and they were really lovely.
Hi Kate, i was wondering if i could use 2 cups shredded apples instead of 1 cup shredded and one cup cubed.
Hi Jenna! I believe that is what another reader did and had luck. Let me know how it goes for you.
Thanks i’ll give it a try.
What if you don’t have applesauce? Should I add more eggs or oil?
Hi Rochelle, These were specifically designed to use apple sauce to help withe the flavor and consistency. You could try adding some more oil as other readers have replaced oil with applesauce in some of my other recipes. If you try it, let me know!
What if I don’t have any yogurt?? What can be used as a replacement??
Hey Stephanie! You’ll find a milk-based option in the recipe notes under the vegan heading. Any milk will do.
What can you use instead of the plain Greek yogurt? I am dairy free.
Hi Diana! See the notes for my vegan/dairy free alternatives below the recipe. I hope this helps!
Hi Kate,
I have mixed up the batter and am so excited to make these! But alas, all I have is a mini muffin tin.
Do you have a recommendation for adjusting baking time / temperature accordingly?
Thanks so much for this and all of your recipes – and sorry if my question has already been asked!!
Thank you for your question, Lizze! You actually don’t need to adjust the temperature. You just need to cut the time by half. I also recommend keeping an eye on them so they don’t get overdone. I hope you love them!
Hi! Can I use spely flour in thsi recipe? Also – change all the yogurt into apple sauce?
Hi Inbal! I haven’t tried this with spelt flour and don’t think replacing the yogurt with applesauce would work. The yogurt helps with the moisture, texture and overall flavor. Applesauce wouldn’t have the same impact.
Hi Kate! Just made these and they were delicious. Thanks for another great healthy recipe. They were just the thing for a snack. Hope you and Cookie are well! P.S. I had a dog named Cookie too :)
Thank you for letting me know, Joy! All my best to you and your Cookie. Mine is curled up right next to me now. :)
Great recipe. Substituted almond butter for applesauce which I think made richer. As I am diabetic substituted agave syrup for maple
Syrup/honey as lower GI. Happened to use strawberry Greek yoghurt as had to hand and didn’t taste odd. Didn’t raise blood sugar too much but tasted like a pretty sweet treat!
Cooked at 375 for 20 mins
Absolute winner! These muffins are amazing. I used vanilla yoghurt as that’s all I had and they are hands down the best apple muffins I’ve ever made!! Could not recommend them more highly. You are a genius!
I made this recipe today without the Greek yogurt (I ran out yesterday!) and without the sugar sprinkled on top to save on calories. I also used olive oil and honey instead of the coconut oil and maple syrup. I just followed your original baking instructions instead of the adjusted temp and baking time for using honey and they turned out great! The muffins were moist and delicious. I will definitely make these again, but may experiment to figure out how to lower the calories a bit per muffin. Thanks for a yummy recipe!
I’m glad it worked out well for you, Holly! Way to get creative. Thank you for your review.
Hi Kate ,
Can I replace honey with an over ripe banana? Without compromising the sweetness .
If so , can you tell me the measurements for banana in cups.
Ps. I recently tried you healthy carrot muffins & banana coconut muffins.. and I have to say they were phenomenal !
Thankyou for the wonderful recipes :)
Hi Saira! I’m glad you’re enjoying my muffin recipes. If you use banana in place of the honey, I’d limit it to the amount of honey called for here (1/2 cup). Otherwise, you’ll disrupt the moisture balance. The muffins will taste like apple-banana muffins and won’t be as sweet.
I made this for the first time a few weeks ago, and have since made it about 5 times as they are SO delicious and flying out of the kitchen aha. I also tried them with gluten free flour for my celiac father, and works great because there’s so many ingredients to add moisture to the batter (often a big fail for me when converting recipes). Thanks for an awesome recipe!
Great recipe kids loved them. I swapped out the greek yogurt and used natural coconut yogurt for dairy free, tasted great
I tried the healthy apple muffins today, it was delicious and we finished it in a jiffy :-) Thanks for sharing this healthier alternative.
They are delicious. My husband and I both ate two with our afternoon tea. I will definitely be making again.
Another wonderful muffin recipe. I love how much apple goes into these muffins and they are so moist and tasty and healthy. They make the perfect snack. I’ve only made the pumpkin muffins and now the apple muffins, but I am hooked. I am going to try all of your muffin recipes. Thanks so much Kate!
Hi Kate,
Love your recipes!
I haven’t been able to find whole wheat flour in Australia. Is it known by a different name here? Also can you substitute for all purpose flour?
Thank you,
Laura
Hi Laura! It might also be called wholemeal flour, if that helps. Yes, you can pretty much always use all-purpose flour in its place (sometimes swapping in the opposite direction is more tricky).
Absolutely brilliant recipe, didn’t make any adjustments, followed the recipe to the tea and result was wonderful….these are unlikely to last more than a day in our house! Thank you for all your wonderful recipes.
You’re welcome, Fritzie! I appreciate your review.
Best apple muffins by far. Got rave reviews from neighbors, the homeless shelter that put one in each “take out” breakfast bag. I’ve made them over and over. THANKS!
You’re welcome, Judy! Thank you for your review.
Absolutely love this recipe, it is just amazing tastes delicious. Easy to follow instructions and loads of great tips. Would definitely recommend!! <3
Loved this recipe…and pretty healthy for a baked good! I used banana instead of applesauce and low fat Greek yogurt. Mine came out a little undercooked, but excited to try your carrot muffins next.
These are wonderful. The only change I made was using melted butter instead of oil and adding 1/4 cup chopped walnuts. I used maple syrup for sweetener and were perfect!
That’s great! Thank you, Toya.
I make this recipe all the time, it’s delicious! I use 1 cup of Greek yoghurt and skip the applesauce, and it works well. I’ve found that using honey and baking at a lower temp/longer time does not work as well as the maple syrup at a higher temp/shorter time. They are still delicious but don’t have the same springiness!
I’m glad you love it! Thanks for sharing, Tansy.
Rave reviews from my picky health conscious family! Made as written, with a combo of WW flour and AP. Used vanilla Greek yogurt too. Thanks you!
Best muffins ever! Super moist and my husband’s favorite by far. I added chopped walnuts for extra goodness. Didn’t have quite enough 0% fat greek yogurt, so added some low fat sour cream and still delicious.
I’m glad you love them, Laurie!
Kate –
Emily and I made the Healthy Apple Muffins yesterday. I used my apple peeler/slicer/ corer and a paring knife to make the apple chunks. We used all chunks. Lots of raisins and walnuts. We ended up with 18 muffins. We also enjoyed your carrot muffins. Emily found your website, but she is shy about reaching out. We are enjoying staying in and cooking. We walk and I ride my bike daily. One outing a week to pick up curbside groceries at Walmart.
Regards, Richard
Ps. Nice website.
I love that! I’m glad you commented, Richard. Thanks for sharing!
I love these muffins, and all your muffins. Your previous apple muffins had oats as well. Was trying to add them here as well and wondering if you would think any other changes would be necessary if I did? Thanks!
Thanks, Lauren! I believe you could add up to ⅓ cup old-fashioned oats without having to adjust the other ingredients.
We love these!! My kids think these are the best and I love that they are healthy for all of us. Thanks for a winner!
Love these muffins. New favorite! I doubled the yogurt as I didn’t have applesauce. Perfect!
I just made these apple muffins and they are amazing! I had to substitute low sugar vanilla yogurt (thick) and I did not have raw sugar so I used a tad bit of brown sugar mixed with additional cinnamon sprinkled on top. I also added pecan pieces for extra protein and they are very good! Thanks!
I found this muffin recipe after using all my Fuji apples to make applesauce. So I was unable to add grated/diced apples to the batter. I used 1 cup of my freshly made (and cooled) chunky applesauce instead of 1/2 cup. I added some chopped pecans, and apple pie spice to the turbinado sugar topping. 18 mins total bake time. Pretty little muffins that taste delicious!
I’m glad they still tasted good, May! I appreciate you taking the time to review.
These muffins are so, so delicious! Moist and just the perfect amount of sweetness- just what I was pining for!!
Hands down my favourite muffin recipe! I’ve made them almost every week for a few months now!