A Healthy Apple Muffin 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 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 cool 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.
Why we love this Muffin Recipe
Obviously, these muffins are just delicious, but we love them for other reasons too!!!
- Lower Sugar – Lots of muffin recipes are loaded with sugar and sweeteners, these are sweetened with just apples and a bit of brown sugar with some flavorful spices.
- 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
These muffins are made with pantry staples you probably already have on hand.
- Applesauce (you can use store-bought or homemade apple sauce)
- Melted Coconut Oil
- Maple Syrup
- Brown Sugar
- Vanilla Extract
- Nonfat Greek Yogurt
- Eggs
- Almond Milk (you could use oat milk or whole milk as well)
- Bob’s Red Mill Whole Wheat Flour
- Cinnamon
- Baking Powder, Baking Soda , Salt
Substitutions
You can easily substitute many ingredients in this 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 oat 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, it may affect the texture.
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 Healthy Zucchini Bread Muffins if you’re looking for other healthy muffin recipes.
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!
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 Apple Muffins
Making these muffins is VERY simple.
- In a bowl whisk together applesauce, oil, maple syrup, eggs, brown sugar, vanilla, Greek yogurt, and milk. Mix in your dry ingredients.
- Gently fold in the diced apple chunks with a spatula.
- Add muffin liners to a muffin pan. Scoop the muffin batter mixture into 12 muffin cups.
- Bake at 425° for 5 minutes then turn down to 350° for 14 minutes or until a toothpick inserted in the center comes out clean.
I love baking with Bob’s Red Mill products because it’s a brand I trust with high quality ingredients.
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!
You can 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!)
Storage options
Storing: I store these muffins in an airtight container 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!
FAQs
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.
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!
Unless a recipe specifically calls for letting the batter rest, it’s best not to let muffin batter rest!
Any oil that is light in flavor is good for muffins. Vegetable oil or refined coconut oil work well in muffins. I like extra virgin olive oil as well.
Other healthy muffin recipes:
Healthy muffins are the best! Check out these Healthy Muffins, or these:
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 apple chunks 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.
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.
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!
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!
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.
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.
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?
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!
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!
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!
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!
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
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!!
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
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!
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!
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!
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!
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.
Sara says
These were good but too crumbly for me.
The Clean Eating Couple says
Thanks for your feedback, Sarah!
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!
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 🙂
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!
Robynne says
Healthy, wholesome and easy to make!
The Clean Eating Couple says
Thank you Robynne! So glad you liked it!
Amy says
Loved these! Perfect treat for fall!
The Clean Eating Couple says
Thanks, Amy! Glad you liked them!
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!