Healthy Apple Muffins
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Last updated on Nov 04, 2024
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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!
Almost every fall we go apple picking at a local orchard and bring home a ton of apples! I love eating apples with my date caramel sauce or making apple nachos for a quick and healthy snack, but I also love making delicious baked good with fresh apples too. I love making my vegan apple bread and baked apple cider donuts, but these healthy apple muffins are usually my go-to apple recipe!
These muffins are hearty, moist and have the perfect amount of sweetness from the coconut sugar and apple chunks. As with most muffins, they pair great with a cup of coffee like my pumpkin spice latte on a chilly fall morning.
Table of Contents
Why You’ll Love These Muffins
- 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 – the less-processed upgrade for brown sugar. You’ll also use some for the topping.
- butter – a tried and true ingredient for giving muffins that moist and delicious texture.
- 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 gluten-free? To make this recipe gluten-free you could sub in an all-purpose gluten-free 1:1 flour. I like the Bob’s Red Mill Gluten-Free 1:1 Baking Flour.
- 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 Tip!
Use 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.
How to Store Apple Muffins
Let these muffins cool completely before storing them. I recommend storing them in the fridge rather than on your countertop. They’ll last longer and they taste delicious straight from the fridge.
That said, these muffins will last 2-3 days at room temperature, up to one week in the fridge or up to 3 months in the freezer.
Brittany’s Tip!
It’s crucial to let these muffins cool completely before storing them. Always let your baked goods cool completely on a wire rack before putting them into a storage container! If you skip this step, the heat creates condensation/moisture and you’ll end up with soggy muffins. Not exactly what we want!
Frequently Asked Questions
Typically, I like to use a mix of apples that are sweet but tart and firm so that it holds up well to baking – if apples get mushy while baking, it’s a no-go for me! Honeycrisp, Pink Lady, Fuji and Granny Smith are fantastic apples to bake with.
Definitely! These muffins store really well in the freezer. Just let them cool completely then transfer them to an airtight freezer-safe container or bag for storage. They can be stored in the freezer for up to 3 months. To thaw, place them in the fridge overnight.
No! This is totally a personal preference. I typically don’t peel the apples when making these muffins, but if the skin doesn’t bother you then you can totally skip peeling the apples, which will save time! Once the apples are cooked the skin will soften so it’s hardly noticeable.
More Muffin Recipes
- Apple Yogurt Muffins
- Healthy Banana Muffins
- Sweet Potato Muffins
- Vegan Blueberry Muffins
- Almond Flour Muffins
- Cranberry Orange Muffins
- Blueberry Cottage Cheese Muffins
Be sure to check out all of my apple recipes as well as the full collection of muffin recipes here on EBF!
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 aside
- In a medium bowl, stir together the flour, baking soda, baking powder, cinnamon and 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.
- Fold the flour mixture into the wet mixture. Gently stir in the apple chunks.
- Pour the batter into the prepared muffin pan and sprinkle with the brown sugar topping. Bake for 22-25 minutes or until a wooden pick inserted in center of 1 of the muffins comes out clean.
- Let cool on a wire rack for 15 minutes.
- 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.
Video
Notes
- 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 gluten-free? To make this recipe gluten-free you could sub in an all-purpose gluten-free 1:1 flour. I like the Bob’s Red Mill Gluten-Free 1:1 Baking Flour.
- 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.
Nutrition
Nutrition information is automatically calculated, so should only be used as an approximation.
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!