Apple Muffins
- By Jennifer Segal
- Updated October 5, 2025
- 304 Comments
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These wholesome apple muffins are packed with spice and everything nice—think warm cinnamon, tart apples, and crunchy brown sugar tops.

Adapted from King Arthur Flour, these delicious 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 yogurt, so no one could ever accuse them of being cupcakes pretending to be muffins. A full tablespoon of cinnamon, plus a hint of nutmeg and cloves, fills your kitchen with the most amazing smell as they bake. But the best part might just be the muffin tops: the brown sugar topping bakes up into a crunchy, irresistible lid.
If you’d prefer something that you can slice and share, my apple bread has similar flavors and is equally crave-worthy.
“A perfect muffin recipe! The house smelled marvelous, too!”
What You’ll Need To Make Apple Muffins

- Butter: Adds richness and flavor, giving the muffins a tender, delicious crumb.
- Granulated Sugar & Brown Sugar: Sweeten the muffins and keep them moist. A little extra brown sugar gets sprinkled on top before baking for that irresistible crunchy lid.
- Egg: Helps bind the batter together and gives the muffins structure.
- Plain Low-Fat Yogurt or Greek Yogurt: Adds moisture and richness while reacting with the baking soda to give the muffins a nice lift.
- Whole Wheat & All-Purpose Flour: Using a mix of whole wheat and all-purpose flour gives you the best of both worlds—nutty flavor and a pretty, toasty color from the whole wheat, plus a light, tender texture from the all-purpose. (Pro tip: all whole wheat will make the muffins a bit dry. However, if you have white whole wheat flour, you can use that in place of both flours.)
- Baking Powder & Baking Soda: These work together to help the muffins rise and stay fluffy.
- Cinnamon, Nutmeg & Cloves: Warm spices that pair perfectly with apples and make your kitchen smell amazing.
- Apples: Add moisture, natural sweetness, and little pockets of apple flavor throughout. Use firm baking apples that hold their shape—Granny Smith, Honeycrisp, Gala, Jonagold, Jonathan, and Golden Delicious varieties are all great options.
- Jump to the printable recipe for precise measurements
Step-by-Step Instructions
Step 1: Cream the butter and sugars. Combine the butter, sugar, and brown sugar and beat until light and fluffy.

Step 2: Add the egg and yogurt. Beat in the egg followed by the yogurt, scraping down the bowl as necessary. The batter may look a little curdled at this point—that’s normal.

Step 3: Mix in the dry ingredients. Add the flours, baking powder, baking soda, salt, cinnamon, nutmeg, and cloves. Beat on low speed until everything is just combined. The batter will be quite thick at this point—that’s exactly how it should be.

Step 4: Mix in the apples. Add the diced apples to the batter and fold them in.

Step 4: Prepare to bake. Grease a muffin tin with nonstick cooking spray. Then scoop the batter evenly into the muffin cups (it’s easiest to use an ice cream scoop with a wire scraper). Sprinkle the tops generously with brown sugar.

Step 5: Bake. Bake the muffins for about 25 minutes, until golden and a toothpick comes out clean. Let the muffins cool in the pan for about 5 minutes, then transfer them to a rack to cool completely. Because the apples help to keep them moist, the muffins will keep nicely for several days, or you can freeze them for longer storage.

More Muffin Recipes You May Like
Spiced Apple Muffins

Ingredients
- ½ cup (8 tablespoons) unsalted butter, at room temperature
- ½ cup granulated sugar
- ¼ cup (packed) dark brown sugar
- 1 large egg
- 1 cup plain low-fat yogurt or Greek yogurt
- 1 cup whole wheat flour, spooned into measuring cup and leveled off
- 1 cup all-purpose flour, spooned into measuring cup and leveled off
- 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)
For Topping
- 6 tablespoons (packed) dark brown sugar
Instructions
- Preheat the oven to 375°F (190°C). 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 to 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 a little curdled—that's okay.
- 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 to 4 hours on the countertop before serving. To reheat, wrap individual muffins in aluminum foil and place in a preheated 350°F (175°C) oven until warm.
Nutrition Information
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.
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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!!!
Hi Jen;
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!