A Healthy Apple Muffins Recipe that is easy to make and low calorie. Made with cinnamon, greek yogurt & whole wheat flour – they’re so yummy! This post is sponsored by my friends at Bob’s Red Mill.
This post contains affiliate links. As an Amazon Associate I earn from qualifying purchases. Click here to read my policy and more about affiliate links. This post was originally shared in August of 2018 but has been updated.
Apple season = the best season in my opinion. There are few things I love more than baking with apples, whether it’s these muffins, Healthy Baked Apples or Apple Oatmeal!
I’m the type of person that eats apple cinnamon and pumpkin flavored things all year round because I love them so much, but there’s something about enjoying fall flavors on a chillier autumn day that makes them taste even better!
I have so many fond memories of going apple picking every fall with my mom and brother. Usually, we’d go with cousins or friends, and we would come back with WAY more apples than we could ever eat.
Back then we probably would’ve made apple crisp, or baked apples.. but I can tell you if we had made these healthy apple muffins, I would’ve been one happy camper – especially if I got to take them as a snack at school!
Why We Love This Apple Muffins Recipe
Obviously, these muffins are just delicious, but we love them for other reasons too!!!
- Low Sugar – Lots of muffin recipes are loaded with sugar, these are sweetened with just apples and a bit of honey.
- Versatile – You can enjoy these for breakfast, or as a snack. You totally could even warm one up, serve it with ice cream and call it dessert!
- Simple ingredients– You probably have everything you need on hand to make these healthy muffins!
Ingredients for Healthy Apple Cinnamon Muffins
These healthy apple muffins are made with pantry staples you probably already have on hand.
- Apple sauce
- Melted Coconut Oil
- Maple Syrup
- Brown Sugar
- Vanilla Extract
- Nonfat Greek Yogurt
- Eggs
- Almond Milk
- Bob’s Red Mill Whole Wheat Flour
- Cinnamon
- Baking Powder, Baking Soda , Salt
You can find substitutions for all of these ingredients below in the green shaded substitutions box.
Important Note: This recipe was originally published in 2019 but has since been update after many reported the recipe was dry and crumbly. Since then, we have changed the ingredients. If you’d like the original recipe you can find it here.
You’ll also want to have a muffin tin, silicone muffin liners, and a blender.
All of the ingredients for this recipe are easily found on Thrive Market! Click here to get 30% off your first order and a free gift.
How To Make Healthy Apple Muffins:
Making healthy apple muffins is VERY simple.
- In a bowl mix together applesauce, oil, maple syrup, eggs, brown sugar, vanilla, Greek yogurt, and milk.
- Add in whole wheat flour, cinnamon, baking powder, baking soda, and salt
- Gently fold in the apples with a spatula
- Add muffin liners to a muffin tin. Scoop the muffin batter into 12 muffin cups.
- Bake & enjoy!
I love baking with Bob’s Red Mill products because it’s a brand I trust. My pantry is always overflowing with their products, but their Whole Wheat Flour is my favorite.
By now I’m sure you’ve seen me use their flour in these Healthy Banana Muffins or Healthy Pumpkin Bread or their regular flour in the Italian Cream Pie!
Apple Muffins Healthy Recipe Substitutions
You can easily substitute many ingredients in this skinny apple muffin recipe. Here are some suggestions for you.
Applesauce: We don’t recommend substituting the applesauce. Banana or pumpkin might work but we can’t recommend it.
Oil: You can use extra virgin olive oil, vegetable oil, avocado oil, or melted butter.
Maple Syrup: You can substitute maple syrup for honey
Brown Sugar: You can substitute coconut sugar but it is not as good! Brown sugar and coconut sugar have the exact same amount of calories.
Nonfat Greek Yogurt: We do not recommend substituting Greek yogurt in this recipe. It tenderizes the whole wheat flour and works as buttermilk would.
Egg free: I have not tried making these muffins egg free. I think subbing flax eggs would work, but I’m not sure.
Milk: You can use any regular milk or nut milk in place of the almond milk
Whole Wheat Flour: We don’t recommend using other flours in this recipe. Bob’s Red Mill Gluten Free 1:1 may work but we haven’t tried it so can’t be sure.
Apples: We haven’t tried this recipe with other fruit but I think pears would work interchangeably here. You can check out our Healthy Blueberry Muffin Recipe or The Best Healthy Zucchini Bread Muffins if you’re looking for other healthy muffin recipes.
If I was you, I’d make these Healthy Apple Muffins STAT!
You can even double the batch and freeze half of them for the school year.
They’re perfect for defrosting in the microwave, slathering with peanut butter, and heading out the door with (or enjoying in the afternoon with a cup of coffee… or pumpkin spice latte!)
What kind of apples are best for baking?
ANY apple will work for baking, but different apples have different tastes.
If you prefer sweeter apples, Cortland or Fuji are a good choice. For a more tart applesauce Braeburn, McIntosh are a better choice.
This post lists all of the different apples and flavors they bring to a dish.
There’s really no ‘wrong’ apple to use – when you bake apples they become softer, sweeter + sooo delicious!
How to Store and Freeze Healthy Apple Muffins
Storing: I store these muffins in the fridge for up to a week to maintain freshness. You can leave them out of the fridge on the counter, but they will only last about 3-4 days.
Freezing: You can freeze these muffins and they will last for about 3 months in the freezer. Put the muffins in an airtight container or ziploc bag. To defrost, leave out the night before in the fridge and they will thaw out. Or – just pop it in the microwave for 1-2 minutes!
Apple Muffin Recipe FAQ
ANY apple will work for apple muffins, but different apples have different tastes. If you prefer sweeter apples, Cortland or Fuji are a good choice. For a more tart apple Braeburn, McIntosh are a better choice.
The healthiest muffin to eat is one that is loaded with whole grains, fresh fruit, and low in sugar! These apple muffins are delicious and good for you!
Having your ingredients at room temperature can help make your muffins light and fluffy. Not over mixing the batter can also help create a light, fluffy muffin.
The secret to moist muffins is a mix of healthy fats, the right type of flour, and not over mixing your batter!
Other healthy muffin recipes:
Healthy muffins are the best! Here are some of our favorite recipes:
Healthy Apple Muffins
Ingredients
- ⅓ cup applesauce
- ⅓ cup melted coconut oil
- ⅓ cup maple syrup
- ¼ cup brown sugar
- 2 teaspoons vanilla extract
- ⅓ cup nonfat Greek yogurt
- 2 eggs
- ¼ cup unsweetened vanilla almond milk
- 2 cups Bob's Red Mill Whole Wheat Flour do not use stone ground version
- 1 teaspoon cinnamon
- 1.5 teaspoons baking powder
- ½ teaspoon baking soda
- ⅛ teaspoon salt
- 2 cups apples thinly sliced then chopped into small pieces about 2 apples -you don’t want chunks
Instructions
- Preheat oven to 425.
- In a bowl mix together applesauce, oil, maple syrup, eggs, brown sugar, vanilla, Greek yogurt and milk.
- Once it’s combined add in the 2 cups of whole wheat flour (add half cup at a time until just mixed), cinnamon, baking powder, baking soda, and salt
- Gently fold in the apples with a spatula
- Optional: Mix together topping ingredients
- Add muffin liners to a muffin tin. Spray with cooking spray for good measure . These muffins rise high and the edges can stick if you don’t spray the whole tin.
- Scoop the muffin batter into 12 muffin cups.
- Add the streusel topping just evenly distributing it onto each muffin.
- Bake at 425 degrees for 5 minutes then turn the oven down to 350 for 14 minutes or until a toothpick inserted in the center comes out clean. Important: the different temperatures allow this muffin to rise high!
- Allow to cool for 15 minutes on a wire rack. Enjoy.
Video
Notes
Nutrition Facts
Important Note: This recipe was originally published in 2019 but has since been update after many reported the recipe was dry and crumbly. Since then, we have changed the ingredients. If you’d like the original recipe you can find it here.
Dana Bacon says
I loved this recipe! Normally I find recipes online and alter them a little, but these were perfect. I added some chopped pecans on top, but they would be delicious without them too. Perfect breakfast slathered with peanut butter. Thanks for the recipe! I am excited to try your other recipes! 🙂
The Clean Eating Couple says
Oooh I love the addition of pecans, Dana!! I’m totally trying that next time I make these 🙂
Taryn says
Made these last night. Used quaker rolled oats because that’s what I had on hand. They turned out good taste wise but the texture is very crumbly. Any idea why this would happen? Yours in the picture look more muffin like than mine.
The Clean Eating Couple says
Hi Taryn – Did you pulse the oats until they were a flour like consistency? That is key to getting the batter right!
Daniela says
I made these this morning and they were absolutely delicious. I don’t have a very big sweet tooth but they satisfied the one I have.
The Clean Eating Couple says
So glad you liked them, Daniela! They’re just the perfect amount of sweetness!
Marie says
Hi! That sounds great. Do you have to use almond milk or could you use regular milk?
The Clean Eating Couple says
Hi Marie – there’s a note about substitutions in the post. You can use nondairy or dairy milk. Either will work!
ratika says
hi! does it matter what kind of apples? I have a mix of green apples and gala apples. thanks!
The Clean Eating Couple says
Nope! Any apples will work – there are notes in the post talking about the different types of apples.
Summer says
These are awesome!! One of the best I have found! I used apples and pears and both were great. I also used oat milk due to a nut allergy and it seemed to work just as well. Thank you!
The Clean Eating Couple says
I’m so glad you liked them Summer! They’re the perfect fall treat!
Kaitlyn says
These are great! I made them for my husband to have in the mornings. If I wanted to add sugar or sweetness, how much would you reccommend adding?
The Clean Eating Couple says
Hi Kaitlyn – I created these muffins without sugar because I think they’re sweet enough without added sugar! You could try adding more honey or 1/4 cup of sugar – but it’s not something I’ve tested and I don’t know how it would affect the outcome!
Katie says
I made these muffins with GF oats and they were amazing! Overall hit by everyone! I will definitely be making these apple muffins again 🙂
The Clean Eating Couple says
So glad you liked them Katie!! Makes me so happy to hear!
Julie says
Delicious and a big hit with the kids. One had with peanut butter and one with almond butter and they both wanted more! Love that these are delish but also healthy! Bravo.
The Clean Eating Couple says
So glad you and your kids liked them!! They are delicious on their own or with any type of nut butter!
Kayla says
These are delicious! Perfect fall treat 🍁
The Clean Eating Couple says
So glad you like them, thanks Kayla!
Wendy says
Moist and delicious! Easy to meal prep for the week
The Clean Eating Couple says
So glad you like them, Wendy! Thanks!
Kady Torres says
I loved these muffins! They are quick, easy and above everything else – pretty good for you. I admit I did serve mine with a little scoop of vegan vanilla ice cream + coconut whipped cream but these are also amazing on their own!
I am Vegan so I subbed out the egg with apple sauce and used Steel Cut Oats from TJs, but I loved these and have made them several times 🙂
The Clean Eating Couple says
So glad you like them, Kady. I LOVE that you served them with ice cream – i bet that is delicious. Have you tried my ? It’s also delish with a scoop of ice cream, and vegan!
Jenn says
These are so easy to make and delicious!
The Clean Eating Couple says
Thank you!! They’re one of my favorite muffins!
Joy Kirkreit says
These are super delicious and easy to make! 🙂
The Clean Eating Couple says
Glad you liked them, Joy!
Charisa R Sloan says
I haven’t made these yet but would like to try, however, I am not big on chunks of fruit in my food. I don’t eat pie just for that reason. Is there a way to substitute the apples for unsweetened applesauce?
The Clean Eating Couple says
Hi! I can’t be sure how this would work without trying it. I don’t think you would need 1.5 cups of applesauce, maybe only 1 cup? I’d recommend you check out this Healthy Banana Muffins recipe and sub in applesauce for the banana. Applesauce and mashed bananas can be used interchangeably, but applesauce and chopped apples aren’t the same so I’m not confident on how it will turn out! Sorry!
Bernadine says
Absolutely would recommend this recipe! Delicious and flavourful. Next time I might add raisins and nuts.
The Clean Eating Couple says
Thanks, Bernadine! So glad you liked them. That would be delicious!
Carlos Gómez says
What is the size for the cups you are using on this recipe?
The Clean Eating Couple says
Hi Carlos – I’m not sure what you’re asking. These are made in a standard muffin tin.
Indigo says
HI Im thinking of making these but do not have any coconut oil. You mentioned in substitutions about using olive oil, which I have, but will it give off an olive-like flavour or not? Thank you x
The Clean Eating Couple says
Hi Indigo – If you use a light olive oil it should’t affect the flavor. Vegetable oil will also work!
Patricia says
Hi! Have made these twice and have liked them. But both times they seem not compact enough (they fall apart very easily). Any thoughts on how I may improve that? Thanks so much!
The Clean Eating Couple says
Hi Patricia – They’re definitely a more crumbly muffin. Did you substitute any ingredients? Maybe try adding a bit more oil. (1/2 teaspoon) and see if that helps. I’m not sure why that would happen!
Patricia says
Thanks! Did not substitute. Will try this improvement. They are very tasty! Thanks many!!!
Dana says
I want to make this recipe for my kids. In the recipe, it says that it makes 18 muffins. I live in Canada and the standard size of muffin tin is 12 and not 18. Would this recipe work for the muffin tin with 12 muffins? Do I need to change bake time? Thanks.
The Clean Eating Couple says
Dana – Use a regular muffin tin, make a batch, take them out, and put 6 in for a second batch. The batch with 6 may cook in 1-2 minutes quicker 🙂
Kristin Kolat says
I made a batch of these on Sunday and they were delicious! Relatively quick to make and came out lightweight, moist and delicious! Perfect for breakfast, snack or dessert. Even my picky father (whom I gave some to) called me to tell me how good they were! I love that he could enjoy them despite being a diabetic given the low sugar/carb content in these!
The Clean Eating Couple says
So glad you liked the, Kristin! Thank you so much!
Sarah says
Hi, is there a sub for applesauce? I don’t have any on hand and don’t have enough apples to make some applesauce. Thanks, Sarah
The Clean Eating Couple says
I’m sorry but we haven’t tried making this recipe without the applesauce. Bananas might work but they will definitely affect the flavor.
Courtney says
I don’t see applesauce in the recipe? Has it been updated or am I missing something?
The Clean Eating Couple says
There is no applesauce in this recipe – I’m not sure what you’re referring to!
Sami says
So yummy and so naturally sweet! I had a lot of fun making these with my Mother in Law last weekend. Added peanut butter on top for a fueled breakfast muffin, and cinnamon sugar for a dessert muffin.
The Clean Eating Couple says
So glad you enjoyed them! Thank you so much, Sami!
Natalie says
I love the idea of these since I can’t have dairy right now, but they turned out very dry for me. Wondering what I can do to add some more moisture,
The Clean Eating Couple says
I’m sorry to hear that, Natalie. Did you make any substitutions? If anything, from feedback I’ve gotten these muffins are more moist than dry!
Stephanie says
Delicious, quick and easy! Both of my toddlers loved them!
The Clean Eating Couple says
So glad you all liked them, Stephanie!
Amber says
So glad I found this recipe. Used dairy milk and all other ingredients as written (I’m notorious for altering recipes!). I used Macintosh apples because that’s what I have leftover from making applesauce. Even though they are a softer apple, I think they did well in this. They are pretty sweet. I love that there is no flour or processed sugar. Even the coconut oil added a nice touch.
I will note that beginning to end was 1 hour for me. Maybe I take too long prepping? But, even then, it was an easy recipe and 26 muffins were done in 20 minutes! Thank you!
The Clean Eating Couple says
Glad you liked them, Amber! Prep time should take about 15 minutes, and they bake for another 15-20!
Meg says
Best fall muffins I ever had!!! Can’t even believe it’s healthy!
The Clean Eating Couple says
So glad you liked them, Meg! Thank you so much!
Carleigh says
These are SO good! And so easy to make! They keep well in the fridge and are great for breakfast.
The Clean Eating Couple says
Thank you so much, Carleigh! I am so glad you like them! They also freeze well if you ever want to double a batch!
Amy says
Loved these! Perfect treat for fall!
The Clean Eating Couple says
Thanks, Amy! Glad you liked them!
Robynne says
Healthy, wholesome and easy to make!
The Clean Eating Couple says
Thank you Robynne! So glad you liked it!
Faye says
I’m looking forward to trying these tomorrow. I have oat flour on hand and would like to use that up. Would I do a cup to cup msmt for the oats? Any idea of how the texture would be affected if I did thick grated apples instead of chunks? I imagine I’d have to squeeze off some of the extra juices? And last question – can I use a ready made apple pie spice in place of all the listed spices? And how much? Thank you in advance.
The Clean Eating Couple says
I’m sorry, Faye – but I don’t have the answers to these questions. The recipe has only been tested as written/with the substitutions we noted. From research I just did: 1 cup whole rolled oats yields about 3/4 cup flour. So maybe try 1.5 cups flour? I can’t give advice on grated apples as I don’t know how that would affect the texture but squeezing out the juice seems smart. I haven’t tried apple pie spice in these but maybe 2 teaspoons would work? I’m sorry but without trying it I can’t guarantee it will work!
Hayley says
These muffins are so delicious! I’ve made them twice now and they’re even better the second time! It seems like a lot at first to have to blend the oats but it’s not hard and doesn’t take a long time. I love that they are healthy! My boyfriend loves them, he will eat about 5 in one sitting! Lol I highly recommend these!
The Clean Eating Couple says
Thanks, Hayley! So happy you both like them 🙂
Carleigh says
These keep you fuller so much longer than regular muffins!
The Clean Eating Couple says
That’s so awesome to hear, thank you!
Sara says
These were good but too crumbly for me.
The Clean Eating Couple says
Thanks for your feedback, Sarah!
Heather Valois says
Do you think it would be ok to swap 1/2 the oil w Apple sauce?
The Clean Eating Couple says
I’m not sure because I’ve never tried this, Heather. Sorry but I can’t be sure without testing.
Ashley says
I love these muffins; not only are they good but macro friendly! I’ve made them a few times and they are great for morning snack.
The Clean Eating Couple says
Thanks, Ashley! So happy you like the muffins!
Alicia says
Perfect snack for my mid-day craving! The peanut butter on top sealed the deal for me! Easy to make and my daughter approved too!
The Clean Eating Couple says
So happy you both liked them!
Jessica says
These are great! I made them with vegetable oil instead of coconut and dairy milk instead of almond since that’s what I had, but still fairly healthy and delicious. Even my fiance who isn’t into health food really enjoyed them!
The Clean Eating Couple says
Thanks, Jessica! So glad you like them!
Chrissy says
I just made these and my son and I think they are wonderful! He said “There is no way these are healthy- they are too good!”
The Clean Eating Couple says
Love hearing that, Chrissy!
Noodles says
I just made these to cure my muffin craving (diets stink!). LOVE them! My only complaint would be that they tend to stick to the paper liners. But that could be that I didn’t let them cool all the way before enjoying.
The Clean Eating Couple says
So glad you liked them! We recommend using silicone muffin liners to avoid sticking. These are a moist muffin so they might stick a bit
Camille says
If I already have oat flour, how much do I use?
The Clean Eating Couple says
I’m not sure because I haven’t tried it but I just searched on google and found that 2 cups of whole oats will usually lead to 1.5 cups oat flour. Hope this helps!
Lisa Hernandez says
Thanks you answer my question. So you can just disregard! Thank you!!
Kim Adda says
Hello! I just made these but I didn’t have a blender so I used whole rolled oats. It worked fine! I also made them lower calorie by replacing honey with sweetener and I added fat-free Skyr yogurt and blueberries as well to the mix. I left out the spices since my partner hates the “american” apple cinnamon flavour (silly man). I used low fat butter spread instead of coconut oil so my fat was only 180 calories total. I made them in a mini muffin tin and it made about 30 muffins. I calculated the calories and I get 46 calories per muffin, I am not sure how you are getting 97 for a full size muffin using coconut oil and honey and I am guessing 2% milk?
These are really good and I do plan of freezing them! Great for a snack when on a calorie deficit diet.
Kim Adda says
Also I see people are complaining they stick, I used a 1 calorie sunflower oil spray and they were absolutely fine. No muffin papers!
The Clean Eating Couple says
Hi Kim – you used completely different ingredients than I did so your nutrition facts are going to be totally different from mine. You also made mini muffins instead of regular muffins so that is why there is a difference in this. Without knowing the exact ingredients I can’t compare the nutrition facts! Glad you liked them
Jennifer says
This is An INCREDIBLE RECIPE
I JUST MADE IT AND MY 15 months old ate 3 mini ones !
I should’ve made a double batch
Next time I’ll add an extra apple and I used maple syrup instead of honey
just AMAZINNNNG
grateful to have this recipe thank you for sharing
The Clean Eating Couple says
So glad you liked it, Jennifer!
Jennifer says
I have a quick question it’s very fluffy and crumbly so when my baby eats it goes everywhere do you think substituting the oats will help it not be as crumbly and messy for me to clean after hahaha
I make these every week ❤️
The Clean Eating Couple says
I’m sorry but I can’t offer substitutions on flour.I’m not sure what you could substitute the oats with/how it would affect the muffins. If you try it let me know!
Amy says
Made these today with just cinnamon and vegetable oil instead of coconut and they are super yummy !! Will make again!
The Clean Eating Couple says
So glad you liked them, Amy!
Elizabeth says
I am obsessed with this recipe! I have made them with added walnuts, raisins, and blueberries. Also substituted ripe banana for the apples. Quick, easy, delicious and healthy!
The Clean Eating Couple says
So glad you liked them, Elizabeth! Thank you!
Dayna Gallagher says
These were SO GOOD! I’ve made a lot of gluten free muffins and I’ve got to say these are in my top 3. So tender! I did use pre-ground oat flour (1 1/2 cup), because I never get good results in the blender despite having a high-powered one. I used pumpkin spice for the spices and subbed out 1/4 cup of the oat flour for buckwheat flour because I like the nutty flavor.
For me, this made 12 big muffins and took about 26 minutes to bake.
The Clean Eating Couple says
So happy you liked them, Dayna! Thank you!
Lisa Hernandez says
I’m going to make these now but I already have some oat flour. Do I still use 2 cups or is it less?
Katie says
Is it 2 cups of oats and then you pulse that amount to a flour OR do you need enough oats to make 2 cups of the oat flour?
The Clean Eating Couple says
Per the directions, you take 2 cups of oats and pulse them into flour.
sydney st-germain says
Did you have an apple muffin recipe with oat, clove and nutmeg? I can’t seem to find it anymore
The Clean Eating Couple says
We changed this recipe to make it better. We were getting a lot of comments saying they were mushy and crumbly with the oats. The old recipe can be found at the very bottom of the blog post.
Kim says
These are my favorite! Easy to make and suoper delish, they make a great breakfast, snack, dessert, etc! I love them with peanut or nut butter!
Rosanna says
What a yummy muffin!
Only change: I sautéed the chopped apples with a touch of sugar and cinnamon to soften.
Also eliminated topping.
Big hit💕
The Clean Eating Couple says
I happy you liked it, Rosanna! Thank you!
Ellen says
These muffins were AMAZING! The batter also tastes delicious. I only did a cup of apples because I’m not a huge fan of fruit chunks and found it to be the perfect amount for me! I will definitely be making these for friends and family in the future.
Kelly says
LOVED these. I added some chopped walnuts to the mix b/c I love nuts in my muffins. I also added some rolled oats to the streusel topping and it was crunchy and so good!!!!
The Clean Eating Couple says
So happy you liked them!
Megan says
Very good. Easy to put together. They were soft and sweet. I followed the recipe exactly. I might cut back on the sugar or syrup next time. I like muffins that are barely sweet, but that is just a personal preference. My husband and two toddlers loved them. I will make them again.
Gail says
Can I use regular yougurt instead I live in canada and greek yougurt is too expensive.
The Clean Eating Couple says
I think that would work! I haven’t tried it so I’m not sure!