Healthy Apple Muffins
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Healthy Apple Muffins that are 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 flavored baked goods 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.
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. You probably have everything you need on hand to make these healthy muffins!
Enjoy these for breakfast or as a snack. You totally could even warm one up, serve it with ice cream and call it dessert!
liz’s top tips for healthy apple muffins
- Don’t overmix your batter for light and fluffy muffins.
- You can double the batch and freeze half of them for the school year for an easy after-school snack kids will love. You can do the same with our pumpkin spice muffins.
- They’re also 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!)
Ingredients
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.
Substitutions
You can easily substitute many ingredients in this recipe. Here are some suggestions for you.
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.
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 dairy 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.
Protein: If you are looking to up your protein intake, try our Apple Protein Muffins.
How to make healthy Apple Muffins
- In a bowl whisk together applesauce, oil, maple syrup, eggs, brown sugar, vanilla, Greek yogurt, and milk. Stir 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!
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, honeycrisp, or Fuji are a good choice. For a more tart apple muffin, granny smith apples, 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!
Storage options
Storing: I store these healthy apple cinnamon 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!
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
- 1 teaspoon ground 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
Streusel Topping (Optional)
- 1 tablespoon melted butter
- 1 teaspoon ground cinnamon
- 1/4 cup sugar
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.
Best fall muffins I ever had!!! Can’t even believe it’s healthy!
So glad you liked them, Meg! Thank you so much!
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!
Glad you liked them, Amber! Prep time should take about 15 minutes, and they bake for another 15-20!
Delicious, quick and easy! Both of my toddlers loved them!
So glad you all liked them, Stephanie!
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,
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!
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.
So glad you enjoyed them! Thank you so much, Sami!
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
I’m sorry but we haven’t tried making this recipe without the applesauce. Bananas might work but they will definitely affect the flavor.
I don’t see applesauce in the recipe? Has it been updated or am I missing something?
There is no applesauce in this recipe – I’m not sure what you’re referring to!
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!
So glad you liked the, Kristin! Thank you so much!
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.
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 🙂
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!
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!
Thanks! Did not substitute. Will try this improvement. They are very tasty! Thanks many!!!
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
Hi Indigo – If you use a light olive oil it should’t affect the flavor. Vegetable oil will also work!
What is the size for the cups you are using on this recipe?
Hi Carlos – I’m not sure what you’re asking. These are made in a standard muffin tin.
Absolutely would recommend this recipe! Delicious and flavourful. Next time I might add raisins and nuts.
Thanks, Bernadine! So glad you liked them. That would be delicious!
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?
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!
These are super delicious and easy to make! 🙂
Glad you liked them, Joy!
These are so easy to make and delicious!
Thank you!! They’re one of my favorite muffins!
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 🙂
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!
Moist and delicious! Easy to meal prep for the week
So glad you like them, Wendy! Thanks!
These are delicious! Perfect fall treat 🍁
So glad you like them, thanks Kayla!
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.
So glad you and your kids liked them!! They are delicious on their own or with any type of nut butter!
I made these muffins with GF oats and they were amazing! Overall hit by everyone! I will definitely be making these apple muffins again 🙂
So glad you liked them Katie!! Makes me so happy to hear!
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!
I’m so glad you liked them Summer! They’re the perfect fall treat!
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?
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!
hi! does it matter what kind of apples? I have a mix of green apples and gala apples. thanks!
Nope! Any apples will work – there are notes in the post talking about the different types of apples.
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.
So glad you liked them, Daniela! They’re just the perfect amount of sweetness!
Hi! That sounds great. Do you have to use almond milk or could you use regular milk?
Hi Marie – there’s a note about substitutions in the post. You can use nondairy or dairy milk. Either will work!
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.
Hi Taryn – Did you pulse the oats until they were a flour like consistency? That is key to getting the batter right!
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! 🙂
Oooh I love the addition of pecans, Dana!! I’m totally trying that next time I make these 🙂