Healthy Apple Muffins
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These healthy apple muffins are made with whole wheat flour and sweetened with coconut sugar. They’re packed with fall flavor and extra moist thanks to pumpkin puree!
Every fall without fail, we end up coming home from the apple orchard with way more apples than we know what to do with. I love making my healthy apple crisp with them, but when I want something I can grab on the go all week, these healthy apple muffins are always my first move.
The secret to how moist these are is pumpkin puree. I know it sounds unexpected in an apple muffin recipe, but it keeps the crumb incredibly tender without needing a ton of butter, and it adds a subtle warmth that pairs so well with the cinnamon and fresh apple chunks. The cinnamon sugar topping is non-negotiable. It bakes into a lightly crisp, sparkly crust on top that the kids go straight for every single time!
Table of Contents
“Perfect fall muffin! Delicious, moist, and all the fall feels. Both my son and spouse love them. Thanks for the wonderful recipe.”
Why I Love This Apple Muffin Recipe
- Healthier: Unlike traditional muffins loaded with refined flour and sugar, these apple muffins are made with whole wheat flour, coconut sugar, Greek yogurt and pumpkin. They’re packed with wholesome ingredients that make for a healthier treat without sacrificing flavor.
- Perfectly Spiced: The combination of cinnamon, pumpkin and fresh apples gives these muffins the perfect fall flavor!
- Great for On-the-Go: These muffins are portable and perfect for busy mornings. Just grab one as you head out the door, and you’ve got a delicious breakfast or snack.
- Kid-Friendly: Olivia and Tucker are big fans of these muffins! I love adding them to their school lunch boxes for a healthy fall treat.
Ingredients Needed
- whole wheat flour – packed with protein, fiber, vitamins and minerals, it is really easy to bake with and provides and added boost of nutrients! I use Bob’s Red Mill 100% Stone Ground Whole Wheat Flour.
- cinnamon – cinnamon with apple is the ultimate fall flavor combo. You’ll also use some for the topping.
- eggs – the eggs are needed to help provide structure for the muffins so they rise and become nice and fluffy.
- coconut sugar – a less processed alternative to brown sugar with a subtle caramel flavor that pairs perfectly with the apples and cinnamon. You will use it in both the batter and the topping.
- butter – just four tablespoons keeps these muffins rich and tender. Make sure it is fully softened before mixing or it will not incorporate properly into the batter.
- pumpkin – adding some pumpkin to this recipe helps cut back on the amount of butter and amps up the fall flavors! Make sure you use pumpkin puree not pumpkin pie filling! You can also make your own pumpkin puree.
- Greek yogurt – I typically use plain full-fat or low-fat Greek yogurt, which helps keep these muffins moist. No dry muffins here!
- apple – the star of the show! You’ll need about 1-2 apples, peeled and finely chopped into pieces. I typically use Honeycrisp or Pink Lady apples, depending on what I can find.
Find the full ingredient list with measurements in the recipe card below.
Recipe Substitutions
- Flour: If you don’t have whole wheat flour on hand, you can use all-purpose flour.
- Pumpkin: Don’t have pumpkin on hand or want to amp up the apple flavor? You can substitute the pumpkin with applesauce, instead!
- Coconut sugar: You can use brown sugar if that’s what you have on hand.
- Want to make them vegan? Use two flaxseed eggs instead of regular eggs, vegan butter instead of real deal butter and non-dairy yogurt instead of regular Greek yogurt.
How to Make Healthy Apple Muffins
Step 1: In a small bowl mix together your cinnamon and sugar topping. Set aside.
Step 2: Add all the dry ingredients to a large mixing bowl and mix to combine.
Step 3: Add all wet ingredients to a separate bowl. Whisk to fully combine.
Step 4: Gently fold the dry ingredients into the wet ingredients. Then stir in the apples chunks.
Step 5: Pour the batter into the prepared muffin pan and sprinkle with the cinnamon sugar topping.
Step 6: Bake for 22-25 minutes or until a toothpick inserted into the center of a muffin comes out clean.
Brittany’s Tips!
- Do not overmix the batter: Stir the wet and dry ingredients together until just combined, even if there are a few small streaks of flour remaining. Overmixing develops the gluten in the flour and leads to dense, tough muffins instead of light and fluffy ones.
- Make sure your butter is fully softened: Cold butter will not mix properly into the batter and can leave lumps. Pull it out of the fridge at least 30 minutes before you start baking.
- Use the toothpick test: Start checking at the 22-minute mark. Insert a toothpick into the center of a muffin and if it comes out clean or with just a few dry crumbs, they are done. A few moist crumbs are fine but wet batter means they need more time.
- Cool completely before storing: I cannot stress this enough. Putting warm muffins into a container traps steam and creates condensation which leads to soggy muffins. Let them cool fully on a wire rack first.
How to Store Apple Muffins
Let the muffins cool completely on a wire rack before storing. They will keep at room temperature for 2 to 3 days, in the fridge for up to one week, or in the freezer for up to 3 months. I actually prefer these straight from the fridge, the texture firms up slightly and they taste amazing cold.
To freeze, let them cool completely then transfer to a freezer-safe bag. Thaw overnight in the fridge or reheat in the microwave for 30 to 60 seconds.
Frequently Asked Questions
I reach for Honeycrisp or Pink Lady for their sweetness and firm texture. They hold up well when baked and do not turn mushy inside the muffin. Fuji and Gala are also great options. I would avoid Red Delicious since they tend to be too soft and mealy when baked.
Not really. The pumpkin is subtle and mostly acts as a moisture booster rather than a dominant flavor. The apple and cinnamon are what you taste most. If you are on the fence about it, just try it once. I promise you will not regret it.
I recommend peeling them for the best texture. Apple skins can become chewy and tough once baked which is not what you want in a tender muffin.
More Muffin Recipes to Try
If you enjoyed this recipe, please consider leaving a ⭐ star rating and let me know how it went in the 📝 comments below.
Healthy Apple Muffins
Ingredients
- 2 eggs
- 2 cups whole wheat flour
- 1 teaspoon baking powder
- 1 teaspoon baking soda
- ½ teaspoon cinnamon
- ¼ teaspoon sea salt
- ¾ cup coconut sugar, or brown sugar
- 4 Tablespoons butter, softened
- ¾ cup canned pumpkin or homemade pumpkin puree
- 1 teaspoon vanilla
- ¾ cup plain full-fat Greek yogurt
- 1 ½ cups peeled and finely chopped apple pieces, about 1-2 apples
Topping
- 2 Tablespoons coconut sugar or dark brown sugar
- 1 teaspoon cinnamon
Instructions
- Preheat oven to 350°F. Line a muffin pan with cupcake liners or coat with cooking spray.
- In a small bowl, mix together the topping – 2 Tablespoons of sugar with 1 teaspoon cinnamon. Set aside2 Tablespoons coconut sugar or dark brown sugar, 1 teaspoon cinnamon
- In a medium bowl, stir together the flour, baking soda, baking powder, cinnamon and salt.2 cups whole wheat flour, 1 teaspoon baking powder, 1 teaspoon baking soda, ½ teaspoon cinnamon, ¼ teaspoon sea salt
- In a large bowl, mix the ¾ cup sugar with the softened butter until combined. Add the eggs, pumpkin and vanilla. Stir in yogurt.2 eggs, ¾ cup coconut sugar, 4 Tablespoons butter, ¾ cup canned pumpkin or homemade pumpkin puree, 1 teaspoon vanilla, ¾ cup plain full-fat Greek yogurt
- Add the flour mixture to the wet mixture and gently stir until just combined. Don't overmix! Gently stir in the apple chunks.1 ½ cups peeled and finely chopped apple pieces
- Scoop the batter into the prepared muffin pan, dividing evenly between 12 muffin cups. Sprinkle with the cinnamon sugar topping. Bake for 22-25 minutes or until a wooden pick inserted in the center of a muffin comes out clean.
- Let cool on a wire rack for 15 minutes.
Video
Notes
- I highly recommend using silicone or paper liners for these muffins! These make for easy removal and less mess. If you don’t have liners, make sure to thoroughly grease the muffin tins. These are my favorite silicone muffin cups.
- Store leftover muffins at room temperature for 2-3 days, in the refrigerator for up to 1 week or in the freezer for up to 3 months.
Nutrition
Nutrition information is automatically calculated, so should only be used as an approximation.
Like This Recipe? Rate & Comment Below!
Wow. Just wow! These are amazing!! I’ve been struggling to find snacks to bring to my desk job (lately its been cheese sticks & chips 💀) & wanted something more fun & healthier. These came out amazing! I even added protein powder to them & they still tasted great! I wanna try substituting the brown sugar w/ unsweetened applesauce, or doing half parts. Either way, this will be my go-to for work snacks! Thank you so much!
So glad you loved these, Sam! I love that they’re working well as a desk snack and that the protein powder addition still turned out great. Thanks so much for making the recipe and for coming back to leave such a thoughtful review.
I followed the recipe and used the Bobs Red mills gluten free flour. The recipe was so thick I could hardly stir it. It could not be poured into anything. I think your recipes look delicious and try them and have no success
Hi Lynne – I haven’t actually tried this recipe with GF flour, so that might have been the reason your batter was too thick. This batter is on the thicker side, but it shouldn’t be too thick. Sorry to hear it didn’t work out for you!
Multiple basic level problems that made these sadly inedible. I used recipe exactly as written.
1. The texture is nothing like a muffin batter- meaning there is likely not enough liquid, and fat. They came out as sort of dry, lumpy, fritter like little things.
2. Sweetness ratio is not correct: they taste like sort of tasteless bran muffins. I wanted something that tastes like an apple muffin, but healthy.
To remedy this (and since all the comments were so good) I remade it and added 1/4 maple syrup, 1/2 cup heavy whipping cream, 1/4 cup full fat Greek yogurt and 1/4 cup almond flour as well as some sprinkled in coconut sugar to give me the correct “muffin batter” texture and mouth feel. That was of course, completely changing the recipe.
Hi Arielle, I’m sorry to hear these didn’t turn out the way you hoped! I haven’t personally run into issues with the sweetness or texture, and others have enjoyed the recipe as written, but they are meant to be on the heartier side compared to a traditional apple muffin. I’m glad you found a version that works for you though, and I appreciate you sharing your adjustments.
These are good! I used all purpose flour. I wasn’t sure about the pumpkin in there. I thought it would taste like pumpkin instead of apple. But it’s very mild and the apple comes through. I like that these aren’t overly sweet either. Thanks for a great recipe!
Yay! I’m so happy to hear you loved these muffins, Heather. I really appreciate you making the recipe and taking the time to leave a review.
I was looking for a way to use up some leftover pumpkin and found this recipe. Loved these muffins and all of your recipes. They were easy to make and had great flavor.
Woo!! That makes me so happy to hear, Karen. So glad the muffins turned out well for you. Thanks for coming back to share a review, I really appreciate it!
Great recipe. I only put one half cup of coconut sugar and used apple sauce and they turned out great.
So glad the muffins turned out well with less sugar and applesauce! Thanks for sharing and for coming back to leave a review. I appreciate it!
Question- can we subsite the sugar with maple syrup or Lakanto Monk Fruit Sweetner
You can definitely try it, but I’m not sure I would use a liquid sweetener because that’ll likely make these muffins too moist. Let me know if you end up trying it!
Made these for kids lunches this week and they are such a yummy fall muffin. made 12 big muffins! may stretch it to 16 next time but kids like the big tops 🙂
Sounds delicious, Jessica. I am so glad the kids are loving these. Thank you for your review & star rating, I appreciate it!
Yummy muffins – I made with gluten free flour and threw in some fresh cranberries and a big handful of chopped walnuts – they made a nice comforting fall muffin
Really tasty muffins. I decreased the sugar to a half a cup and they were still very good and sweet thanks to the apple and the topping. The pumpkin was a nice touch for moistness and does not overtake on flavour. I will definitely use this recipe again.
I can’t wait to make these. Do you think they can be made with oat flour?
Hi Jennifer. I wouldn’t recommend using oat flour, but you can use all purpose flour instead if you have that available. Enjoy!
Hi
These muffins look delicious! I’m thinking of making them Texas size and eating one for breakfast. Can I substitute some of the flour for protein powder to up the protein? And would it be a 1:1 ratio?
Hi Rosie – I haven’t tried subbing some of the flour with protein powder so I cannot say for sure if it would change the texture of the muffins. Also, depending the type of protein powder, you may need to adjust the liquid due to the absorption. So sorry I can’t be of more help because I haven’t tried it, let me know if you give it a try though.
Love the idea of healthy apple muffins! They’re a great way to enjoy a sweet treat without compromising on nutrition. Thanks for sharing this yummy and wholesome recipe.
Of course! Hope you enjoy!
These are so delicious! My husband normally hates baked goods with whole wheat flour but he’s been wolfing them down
Woo!! So pumped to hear these muffins were a hit. Thanks for making them and for coming back to leave a review. I so appreciate it!
Can you use whole wheat pastry flour?
Totally! That should work fine. Let me know if you end up making these and how they turn out!
These are the BEST muffins I have ever made!!! Seriously delicious and moist, the flavours are so autumnal/wintery and cosy and they were so easy to make! For substitutes I did some of my he ones recommended based on what I had available and used 2 eggs, only plain flour, and used the apple sauce recipe linked instead of pumpkin purée! Thank you for this recipe 😍
Yay!! So happy to hear this muffins were a hit and that the substitutions worked out for you! Thanks so much for the review, Phoebe. I really appreciate it!
I’ve been meaning to make these since I saw them in IG (I’m a big EBF fan!) and finally did tonight. I’m bummed that these were not my favorite. The batter came out very thick and the overall texture of the cooked muffins are very spongy and they really stuck to the liners at the bottom. Maybe if I try them with real eggs and no liners they’ll be better? The flavor and nutritional value are good though.
Oh no!! So sorry to hear that, Lindsay. Did you change anything about the recipe?
Hi there, quick question-the instructions say to add the all purpose flour AND whole wheat flour but the ingredients list only includes measurements for the whole wheat flour. What is the correct measurements for flour? Thanks!!
Sorry about the confusion! You can use either flour or a combo of the two, but I just updated the instructions. 🙂
Made these yesterday for a ladies book study. Not only was I impressed, but my daughter, and 4 other people. Look forward to trying other recipes from your site. Healthy doesn’t have to be boring!
Woo!! So happy these muffins were a success, Joleen! Thanks for the review. I really appreciate it!
Perfect fall muffin! Delicious, moist, and all the fall feels. Both my son and spouse love them. Thanks for the wonderful recipe.
Aw yay! So pumped these muffins were a success, Samantha! Thanks for making them and for the review + star rating. It means the world to me!
This are delicious and moist. I subbed out applesauce for the butter, ripe banana for the pumpkin and 3 egg whites for the 2 eggs. They were a bit dense in texture but that might be the 3/4 c mashed bananas I used. Will be making these again.
Yay! So glad these muffins were a hit, even with the substitutions. Thanks for the review, Cleo! I really appreciate it!
They are so delicious! Super moist, tons of flavor. I subbed the flours with gluten free options (1 cup almond flour, 1 cup 1-1 flour) and they are incredible.
yay!! So glad these muffins turned out for you with the almond + gluten-free flour, Jackie. Thanks so much for coming back to share that, it’s super helpful for future readers. 🙂
Just made these this morning and they turned out AMAZING! I used 2 cups of white whole wheat flour instead of 1c APF and 1c whole wheat flour. My friend also subbed and did 1c oats and 1c flour and it worked out perfectly for her! Also I skipped the topping but I’m sure it would have been delicious. Thank you, Brittany!
Oh yay!! So glad these muffins turned out for both you and your friend. Thanks for sharing what subs you guys made. It’s super helpful for other readers, so I appreciate it. <3
Made these on a fresh fall morning and the family woke up to a delicious smell! I am so glad I stumbled across this recipe, they won’t stop going on about how absolutely delicious these muffins are! (Even a yogurt-hater just adores them!)
Woo!! That makes me so happy to hear. 🙂 I’m so glad these muffins were a hit with your fam. Thanks so much for making these and for coming back to leave a comment + star rating. I really appreciate it.
These muffins are the best!! I was wondering if its ok to put them in the freezer?
Thank you!
Totally! They should store just fine in an airtight container in the freezer. 🙂
Yum!! Super simple to make
always looking for baked goods with whole wheat flour. this recipe came out great and my picky kids can’t get enough. i used the eggs and whole milk greek yogurt, so that didn’t hurt and even used an extra 1/4 cup whole wheat instead of regular. also a huge fan of coconut sugar and pumpkin is always YUMMY. I’m going to try the pumpkin bars next. oh – and love that i didn’t have to use liners. greased tins with coconut oil.
Woo-hoo! So glad you and your kids enjoyed this recipe, Stacy! Thanks for trying it and for coming back to leave a comment and star rating. The ratings are super helpful so I really appreciate it! <3
Brittany, your timing was perfect with the Apple Cinnamon muffin recipe! I am working through A LOT of apples right now and the pumpkin was a great addition! (I confess I also added toasted walnuts – because I’m nuts about nuts!). Even without they are moist and, well, perfect! A huge hit in my house! Making more for the freezer… 🙂
Yay!! I am so glad that the muffins were such a hit. Thanks so much for sharing, Charlane.
I’m just about to make these and I saw there were asterisks after the butter and Greek yogurt. Is there something about them I’m missing. I’m making this with pumpkin so I want to make sure I’m supposed to add butter when using the pumpkin. Thanks! Can’t wait to make them.
The asterisks just mean that there are notes down below about the ingredients. The notes are about how to make the recipe dairy-free. Hope this helps. Let me know how the muffins turn out for you.
Hi Brittany! 🙂
Do you think I can use Almond flour or Coconut flour instead of the all purpose & whole wheat flours?
They look delish!
Hi Nancy! I think you could easily use an all-purpose gluten-free 1:1 flour for the full amount of flour. I can’t speak to coconut or almond because I haven’t tested it. Let me know if you try it and how it turns out for you.
Have you made these with gluten free flours? I would love to try them but would need to make them GF. Do you think I can sub 1:1? I have not substituted with recipes that call for white and whole wheat flours together.
Hi Jeni. I haven’t tried it, but I think you could easily use an all-purpose gluten-free 1:1 flour for the full amount of flour. Let me know if you try it.
How do I remove the black box that advertises a new recipe “get recipe”. The is no “close” option and it blocks the recipe
Ugh! I’m so sorry you’re dealing with this. I’ve contacted my ad network and had it removed.
I don’t have Flaxseed, is there anything else I can use? Thanks 🥰
Hi Dottie. The flaxseed + water combo is a replacement for eggs. If you don’t have flaxseed, just use 2 eggs instead of the flaxseed and water. 🙂
Anyone wanna take a stab at how many calories might be in these muffins? Roughly?
Hi Tara. Just added the nutritional stats to this recipe! They have about 185 cals per muffin.
Could I leave the pumpkin out? Or use something else instead? Maybe butternut squash?
Can I use Oat flour instead of wheat?
I think that would work fine.
So glad you shared this recipe. I’ve been looking for new ways to add a little extra fiber to my diet and these are so delicious. I was cutting them in half and reheating with a little bit of olivio on them but they don’t even need that…they are great on their own. Love them! Thanks!! 🙂
So glad you like them Kristie!
I need to bake me some of these!
This is PERFECT!!!!! I have been scouring Pinterest for a yummy Apple Cinnamon muffin, and here it is! Will be making these sometime soon! Maybe tomorrow?! To celebrate Halloween + being done a midterm! 🙂
The the information you are providing is really helpful to me .keep posting.
I went to UVa so I feel very fondly for that entire area. The hiking, apples, mountains. Sigh. And I also can’t wait to try this recipe!
So cool! I grew up in Orange, VA so I’m pretty fond of that area too. 🙂
We went out to Carter Mountain last weekend and grabbed some of our own. So far I’ve done an apple pie baked oatmeal for breakfast, and HomeMan made a dessert pizza like the ones on pizza buffets with his homemade crust! Whatever we have left will go into crock pot applesauce on Saturday, but I might have to try this recipe out first!
Oh yum – everything you all made sounds awesome. I think I need some apple pie baked oatmeal in my life!
these. look. delicious.
can you send some my way 😉
I would, but they are gone already. 😉
These look so good Brittany! Way better than mine. 🙂 I need to take baking tips from you girl.
These look great, lady!
Thank you dear! We need to catch up soon – I feel like we haven’t seen each other/emailed in ages.
Wondering if these can be baked in a baking pan instead of cupcakes, if so what size pan?
Great question, Debbie! I haven’t tried baking these in a pan myself, but I think an 8×8 or 9×9 baking dish should work well. The bake time might be a little longer, so just keep an eye on it and check with a toothpick in the center. Let me know if you give it a try.
I am a sucker for muffins and anything apple or pumping during autumn, so count me in. I want to try these asap!
LOVE that these don’t have eggs in them 😀 I’m so not a fan of eggs lol apples and cinnamon are prob the best combo in my book, I’ll totally try these out 🙂
apples + cinnamon = <3
I love, love, love all of your healthy substitutions! I have a bunch of apples that need to be used up and I will definitely be using some in this recipe. Can’t wait to try!
Yay! I hope you love them!
These look delicious! I love anything with apple 🙂
Apple + Cinnamon is probably my favorite flavor combination!
Me too!!
These look incredible – I can never get enough cinnamon!