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These wholesome apple muffins are full of spice and everything nice.
Adapted from King Arthur Flour, a wonderful resource for bakers, these apple muffins are made partially with whole wheat flour, which gives them a wholesome, nutty flavor and toasty-brown color. They’re also chockfull of tart apples and enriched with low-fat yogurt, so no one could ever accuse them of being cupcakes pretending to be muffins. The recipe calls for a full tablespoon of cinnamon along with a hint of nutmeg and cloves, so your house will smell amazing while the muffins bake. But the best part of these apple muffins might just be the simple brown sugar topping, which gives the lids an irresistible crunch.
What you’ll need to make Apple Muffins
It’s important to pick apples that are good for baking: Granny Smith, Honey Crisp, Gala, Jonagold, Jonathan, and Golden Delicious all work nicely.
To begin, combine the butter, sugar and brown sugar.
Beat until light and fluffy.
Add the egg.
Then beat again.
Add the yogurt.
Add all the dry ingredients right to the bowl.
Mix until just combined. Note that the batter will be very thick.
Add the diced apples.
Then stir them in.
Use an ice cream scoop to transfer the batter to a muffin tin.
Sprinkle the tops generously with brown sugar.
Bake for about 25 minutes.
Let the muffins cool in the pan for about 5 minutes, then transfer them to a rack to cool completely.
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Spiced Apple Muffins
These wholesome apple muffins are full of spice and everything nice.
- ½ cup (8 tablespoons) unsalted butter, at room temperature
- ½ cup granulated sugar
- ¼ cup dark brown sugar, packed
- 1 large egg
- 1 cup plain low-fat yogurt or Greek yogurt
- 1 cup whole wheat flour, spooned into measuring cup and leveled-off with back edge of knife
- 1 cup all-purpose flour, spooned into measuring cup and leveled-off with back edge of knife
- 1 teaspoon baking powder
- 1 teaspoon baking soda
- ½ teaspoon salt
- 1 tablespoon ground cinnamon
- ½ teaspoon ground nutmeg
- ¼ teaspoon ground cloves
- 2 cups peeled, cored, and finely chopped baking apples (you'll need 2 large apples)
- 6 tablespoons dark brown sugar, packed
- Preheat the oven to 375°F. Grease a 12-cup muffin pan with butter or spray with non-stick cooking spray.
- In the bowl of an electric mixer, beat together the butter, granulated sugar and brown sugar until fluffy, 1-2 minutes. Scrape down the sides of the bowl with a rubber spatula.
- Add the egg and mix well, stopping to scrape the bowl if necessary.
- Beat in the yogurt. The batter will look grainy.
- Add the flours, baking powder, baking soda, salt, cinnamon, nutmeg and cloves. Beat on low speed until just combined. The batter will be very thick.
- Add the chopped apples and mix until just combined. Do not over-mix.
- Use an ice-cream scooper or large spoon to divide the batter evenly among the prepared muffin cups. The cups should be full. Sprinkle the 6 tablespoons of brown sugar evenly over top.
- Bake the muffins for 25 to 30 minutes, or until a toothpick inserted into the center of a muffin comes out clean.
- Remove the muffins from the oven, cool them for 5 minutes in the pan, then turn them out onto a rack to finish cooling completely.
- Freezer-Friendly Instructions: The muffins can be frozen in an airtight container or sealable plastic bag for up to 3 months. Thaw for 3 – 4 hours on the countertop before serving. To reheat, wrap individual muffins in aluminum foil and place in a preheated 350°F oven until warm.
- Serving size: 1 muffin
- Calories: 221
- Fat: 9g
- Saturated fat: 5g
- Carbohydrates: 33g
- Sugar: 16g
- Fiber: 2g
- Protein: 4g
- Sodium: 207mg
- Cholesterol: 37mg
This website is written and produced for informational purposes only. I am not a certified nutritionist and the nutritional data on this site has not been evaluated or approved by a nutritionist or the Food and Drug Administration. Nutritional information is offered as a courtesy and should not be construed as a guarantee. The data is calculated through an online nutritional calculator, Edamam.com. Although I do my best to provide accurate nutritional information, these figures should be considered estimates only. Varying factors such as product types or brands purchased, natural fluctuations in fresh produce, and the way ingredients are processed change the effective nutritional information in any given recipe. Furthermore, different online calculators provide different results depending on their own nutrition fact sources and algorithms. To obtain the most accurate nutritional information in a given recipe, you should calculate the nutritional information with the actual ingredients used in your recipe, using your preferred nutrition calculator.
Can I use 2 cups of whole wheat flour?
Hi Eileen, Using all whole wheat flour may make the muffins dry. If you have white whole wheat flour, that would work. If not, I’d probably go with 1.5 cups of whole wheat and .5 cup all purpose flour. Hope you enjoy!
I noticed there is no need to line the muffin pan, do you mind explaining why? Thank you!
Hi Ana, some muffins are more prone to stick without liners, but I haven’t had a problem with these as long as I thoroughly grease the muffin tin. Hope that clarifies! 🙂
Cant wait to try this recipe. What type of apples work best?
Hi Nan, I’d recommend any of the following (and I’d use one of each for the best flavor): Granny Smith, Honey Crisp, Gala, Jonagold, Jonathan, or Golden Delicious. Hope you enjoy!
My boys love your cinnamon swirl apple bread, so I am excited to make these for them. I have whole milk plain yogurt, will that be okay to use?
Thank you so much
Sure, Melissa, that’s fine. Hope you enjoy!
Hi Jenn – I am so excited to bake these muffins tonight. How much can I reduce the sugar in the recipe without compromising the muffins?
Thank you in advance – my family and I love your recipes!
Hi Taylor, So glad you like the recipes! I think you could get away with cutting a total of 1/4 cup of sugar. I’d love to hear how they turn out. 🙂
Delicious, as always! Thanks, Jenn!
Hi – Can use my cupcake pan for this or do I need to buy a muffin pan? I think the muffin pans have bigger slots.
Yes (they’re actually the same). Enjoy the muffins!
Can I substitute canola oil for butter?
Hi Margot, canola oil won’t work here, but you can use (solidified) coconut oil if you’d like. 🙂
Wow, Jenn. Another great muffin recipe. You have the best muffin recipes ever! I love the banana nut, pumpkin nut and now this. I did it exactly the way you have it and it was delicious.
However, I love nuts and I was wondering if I could add walnuts in it? I was thinking of adding chopped walnuts with honey and cinnamon as a topping. What do you think?
So glad you like the muffin recipes! Yes, I think you could add the topping you’ve suggested. Please LMK how they turn out with it!
Can I substitute sourdough discard for half of the flour?
Hi Marion, I wouldn’t recommend it – sorry!
Hello, we love, love, love the muffins!
How do I best store them and for how long will they hold?
So glad you like them! They should last for several days. To store them, line a sealable container with a sheet of paper towels. Arrange the muffins in a single layer and cover them with another sheet of paper towels to absorb any excess moisture. (And they can be stored on the countertop.)
These muffins are wonderful and they freeze well. Made them several times. Last time I reduced sugar to 80g and added 70g roasted ground nuts for better nutritive balance and it turned amazing.
These muffins are delicious, but they are even better by day #3! Next time I will coarsely grate the apples so they are consistent in size and bake evenly.
Best apple muffin recipe ever!! My husband and I are hooked on them, so I bake them every Sunday, bag and freeze them once they cool off, so we can enjoy them during the week. Thank you!
Can this be made into a cake? If so what adjustments are necessary for the temperature and /or bake time? Thank you – your recipes are wonderful!
Hi Ana, If you want an apple cake, I’d suggest using this recipe. It’s slightly different than this but delicious!
I’ve made your French Apple Cake several times – and it’s AWESOME. The spiced apple muffins were a really big hit this week. Thank you yet again for your amazing recipes!
My family loves these muffins. I bake them when I want something sweet but also “healthy.” I ran out of whole wheat flour so I made oat flour (pulverized old-fashioned oats in a food processor) and the recipe still turned out great. I usually use half the brown sugar topping and the muffins are still tasty. Thanks Jenn!
Why not Greek style yogurt? That’s all we usually have so I’d rather not have to buy regular yogurt that no one will eat.
Hi Nancy, You can use Greek yogurt here but you’ll need to thin it out with a little bit of milk. Hope you enjoy!
Can you use buttermilk instead of regular yogurt? or is it better to use sour cream?
Hi Sharon, I’d probably go with the sour cream, you can use buttermilk also but it may slightly change the texture of the muffins. Hope you enjoy!
I prefer buttermilk over yogurt. Work’s great. Ratio is 1:1. Instead of 1 teaspoon baking soda, 1 teaspoon powder… Go one and a half teaspoon s baking soda, half teaspoon baking powder.
I was missing fall flavors when I made this over the summer and I was not disappointed with this recipe. It turned out amazing and the muffins did not last long in our house.
The muffins were absolutely delicious! The whole family enjoyed them. I will be making them again soon.
Run don’t walk to your kitchen to make these muffins! Tick all the boxes…easy to prepare, spices are totally delicious, and the crunchy top puts them over the top. Keeping this one in my “Jen File” (which is getting really full). Can’t wait for your next cookbook.
Family friendly and really yummy. My house is filled with the most amazing scent right now. Great recipe. I used Greek yogurt thinned out because that is what I had and over mixed the batter and they were still great! . I will try them next time with regular yogurt.
Easy and delicious!
This is the BEST apple muffin recipe I have ever made! My husband loves them. He shared with his co-workers and they said that they were the best apple muffins they ever tasted. I will be making them again and again, and again.
Very good muffin! Didn’t have quite enough flour so added some oats and we really enjoyed them!
These apple spice muffins are delicious! If I want to bake something, Once Upon a Chef is always the first place I turn, because all of Jenn’s recipes are wonderful. I have made these without any substitutions and also by substituting avocado oil for the butter and they turn out beautifully either way.
Had lots of apples and decided to try this recipe. I normally don’t like cooked apples but these muffins were perfect. I decided to try the recipe because I like spice cake. Muffins were excellent without being mushy with apples and spice was not overwhelming either. Perfect ratios, nice and moist too.
can I make this recipe without the yoghurt? what can I use instead?
Hi Rebekah, Sour cream would be a good substitute.
These were delicious! We added a little less sugar and they were still quite sweet. Also, these made 15 muffins for me rather than 12.
I used Greek yogurt because that’s all I had. Thinned it out with probably 2-3 tbsp. of milk, and they turned out perfect. Also made my house smell AMAZING!
I have now made these twice in less than 24 hours!! Delicious recipe, the crumb is perfect and the kitchen smells divine!! Trying internet recipes can be dicey, but this one is a keeper!! YUM!
So delicious! My three year old always asks for these special muffins.
Absolutely love all your recipes. Would love to try the spiced apple muffins but only have my homemade Greek yoghurt. Can I substitute the whey?
Hi Chantal, Glad you like the recipes! I’m not familiar with homemade yogurt, so I don’t know if the lack of whey would make a difference. I’m sorry I can’t be more helpful!
Hi Jen. Can I substitute 2 cups of all purpose gluten free flour for the whole wheat and all purpose flour? Also, what can I use to replace cloves? I love your site and appreciate you expertise.
Hi Kathy, Glad you like the recipes! I think these would work with gluten-free flour (though I haven’t tried it myself). And you can replace the cloves with more cinnamon or nutmeg. Enjoy!
These muffins are delicious! A perfect use of extra apples on hand, and the warm spices really come through—thank you!!!
I’d like to make the Spiced Apple Muffins but I don’t have whole wheat flour. Can I use
all-purpose flour and if so do I have to adjust the amount?
Bythe way, I made the Cinnamon Swirl Apple Bread last week. It was delicious.
Today I bought a cauliflower and will make the Curried Cauliflower Soup.
Hi Doreen, You can definitely use the same amount of all-purpose flour. And so glad the cinnamon apple bread turned out well!
Hi Jenn, I don’t have yogurt on hand. What can I substitute to make these muffins? I live in a community that has no grocery store so it means a trip to get this ingredient. Thanks!
Hi Judy, Sour cream will work nicely in place of the yogurt.
I baked these Spiced Apple Muffins and took them to the Wednesday night class at my church. Everyone loved them. They disappeared before any other goodies. I kept hearing, “They’re so moist. What did you put in these? They’re so good!”
Oh, and if you aren’t going to eat them in a day or two be sure you keep them in the fridge so that the sour cream doesn’t sour.
This is a keeper!
Wow, I’m not a muffin person but these are fabulous. We have an orchard with a variety of apples so I used what was ripe. I think the different textures and tastes made the muffin more interesting. I prefer less sugar and so only used a light sprinkling of topping sugar (2 Tbsp) but it was enough for me. The sugar definitely adds a nice crunch to the muffin so wouldn’t skip it. Thanks!
Awesome recipe I can’t wait to try it out! Can I use pumpkin pie spice if I don’t have clove or nutmeg instead? Thank you!!
Sure. It may give them a slightly different flavor, but it should definitely work. Hope you enjoy! 🙂
Yet another great recipe! Thanks
These were really good.
Just made these and they were very nice….wondering about grating the apples to give an apple flavor throughout every bite and also wondered about adding nuts?
Glad you liked these and I think you could get away with grating the apples and adding some nuts. Please LMK how they turn out!
These muffins are perfection. I don’t typically bake with whole wheat flour and I was a little worried they would be dry or tough but the texture was amazing. The spices were spot on as well.
Another fantastic recipe Jenn! Made these muffins with sour cream since that’s what I had on hand and they were perfect. They actually reminded me of the Hostess Crumb Cakes I loved as a kid, but sooooo much better!
Can you use tinned apples when in a pinch?
I think it would be best to stick with fresh apples for this — sorry!
Once again Jen – You are the queen of cooking. I had my doubts on this as I only had greek yogurt so I added a TBsp of milk to make it a bit more liquid. I didn’t add as much brown sugar on the tops – which still covered the muffin top. I didn’t think they would rise – but they did and they are absolutely perfection. The crumb is perfect, the taste divine – just lovely. You just keep on doing what you’re doing and we all look good:) Thank you again
These were amazing!! I forgot to add the topping so I’ll try to remember that next time, but other than that I didn’t change a thing and the muffins turned out perfect. They came together fast too! Will make many times again.
JENN, what can I use instead of Yogurt in these great muffins?
Hi Christine, Sour cream will work as a substitute for the yogurt. Enjoy!
I would like to make a vegan version of these muffins. What can I substitute for the yogurt that would be vegan friendly?
Hi Patty, Although I haven’t tried it, I would think a vegan yogurt would work here. Please LMK how they turn out if you try it!
Can I use applesauce instead of yogurt?
I wouldn’t recommend it, May as the yogurt helps the muffins to rise. Sorry!
What variety of apples do you like for this recipe? Thanks!
Hi Katie, I like Honeycrisp, Fuji or Granny Smith. Hope you enjoy!
Hi! can I use sour cream instead of yoghurt??
Sure – hope you enjoy!
I made these delicious apple spiced muffins today. They came out excellent. My kids and husband loved them.
Very easy to make and super delicious!!
Can I use whole milk plain yogurt instead ?😊
I used Greek yogurt like you suggested but my muffins did not cook. They all fell in the center and it’s like applesauce and I did use honey crisp apples
Very disappointed. Usually your recipes are great Jen.
It’s says to not use Greek yogurt, but regular low-fat plain
Love all of your recipes! I was wondering can i use full fat yogurt i have a huge thing leftover from making your tikka(which is amazing btw)
Thanks so much
Sure (and glad you enjoyed the chicken)! 🙂
Used only all-purpose flour (2 c total) because that’s what I had. Also, subbed 3/4 c Half & Half for the yogurt because my fridge is basically empty. Added 1/2 c walnuts to the batter and these turned out delicious!!! Will definitely be making again using the yogurt after I finally make it to the store…
I thought the level of sweetness of these was perfect! Love your recipes ❤️