This recipe for hearty, healthy apple muffins has lived on my website since 2016. I’ve made a couple slight changes over the years so they rise taller and have a stronger apple flavor. They’re wonderfully wholesome and soft, and you’ll appreciate that they’re made without any refined sugar. These are my go-to choice when I’m looking for a quick and easy healthy muffin! For a classic and indulgent version, try my apple cinnamon muffins.
I originally published this recipe in 2016 and have since added new photos, a video tutorial, and a few more success tips.
One reader, Eileen, commented: “These muffins are as delicious as they are beautiful… and they’re healthy!… The way the tops rose up was amazing! I will be making these often. โ โ โ โ โ “
Today’s muffins are adapted from my morning glory muffins, which have all sorts of goodies packed inside like grated apple, grated carrot, raisins, nuts, etc. Think: carrot cake, but lightened-up.
For this apple version, we’re leaving out the grated carrot and switching up a couple other ingredients. To keep them on the lighter side, I use a mix of applesauce and melted coconut oil. This way the muffins keep their moist, rich texture but arenโt weighed down with fat.
Here’s Why You’ll Love These Healthy Apple Muffins
- Quick and easy
- No mixer required
- Zero refined sugarโuse pure maple syrup and apples to sweeten
- Use whole wheat flour for hearty, wholesome flavor
- Flavored with cinnamon, allspice, and lots of apples and applesauce
- Absolutely healthy, but they don’t taste like cardboard (not at all bland!)
- Dairy-free recipe
Key Ingredients & Why They Work
- Whole Wheat Flour: I love using whole wheat flour in baking when I can. Whole wheat flour can quickly dry out your baked goods, so it’s important to pay close attention to the wet ingredients. For example, there’s extra butter and milk in these whole wheat dinner rolls to make up for the hearty flour. Today’s muffins are super moist and we have the following listed ingredients to thank!
- Eggs: This recipe used to call for 3 eggs, which weighed the muffins down and provided too much eggy structure. I updated the recipe so you use 2 eggs and more applesauce.
- Unsweetened Applesauce: Just as if you were making applesauce muffins, make sure you use unsweetened applesauce here. If all you have is sweetened, slightly reduce the maple syrup as noted in the recipe Note below.
- Pure Maple Syrup: Pure maple syrup sweetens the muffins and adds some moisture. The darker the pure maple syrup, the stronger the flavor. So if your maple syrup is extra dark with robust flavor, slightly reduce to 1/2 cup (120ml). If your maple syrup is golden or light amber colored (not very dark), use 2/3 cup as instructed below.
- Coconut Oil: Instead of butter or vegetable oil, use melted coconut oil. This is one of my very favorite ingredients in the kitchen and you can use it again for these chocolate banana muffins.
- Shredded Apples: Use shredded apples instead of chunks. Why? Shredded apples act as a wet ingredient while chunks act as an add-in. You want MOISTURE, so grab a grater just as if you were going to shred carrots for carrot cake or zucchini for zucchini bread.
You also need cinnamon, allspice, baking soda, baking powder, and vanilla extract. Chopped pecans or walnuts are optional, but add a little extra texture and flavor.
Today’s muffin batter comes together in just 5โ10 minutes with simple kitchen tools including a couple bowls, a whisk, and a muffin pan. If you’re looking for grater recommendations, I love this box grater because it’s easy to use and has held up well with regular use. If you want to make muffins with apple chunks, try apple cinnamon bread or these equally healthful apple cinnamon baked oatmeal cups instead.
Best Apples to Use
You need about 2 cups of shredded apples, which is about 210g or 2 peeled apples. Feel free to leave the peel on if desired. The best apples to use in these healthy apple muffins are a sweet variety like Pink Lady, Honey Crisp, or Fuji. Or you can use 1 tart apple like Granny Smith and 1 sweet. A combination of flavor profiles can be important in baked goods, especially apple pie or apple crisp.
Healthy Apple Muffins: Helpful Notes
- Expect a thick batter. Thick batter helps ensure the muffins lift UP rather than spread OUT.
- Feel free to replace the allspice with nutmeg. Allspice is one of my favorite spices to use in baking and you can see it used in these peach muffins and these apple hand pies. If you don’t have allspice, don’t worry about itโuse nutmeg instead.
- Add an optional coarse sugar topping. You can use coconut sugar, something like Sugar in the Raw, or sparkling coarse sugar (usually sold as sprinkles).
- Bake at an initially high oven temperature. Bake the muffins for 5 minutes in a very hot oven. Then, keeping the muffins in the oven, lower the oven temperature. This initial high oven temperature quickly lifts up the muffin top. Once the temperature is lowered, the centers of the muffins bake. I do this in all my muffin recipes.
Again, expect a thick batter. You might think you’re doing something wrong but you’re not. This batter is extra thick and that’s expected!
I bake muffins A LOT, usually at least once a week. They’re one of my favorite kid-friendly baking recipes and back to school recipes (easy to mix & quick to bake) and they freeze wonderfully. Banana muffins are a top choice, but these healthy apple muffins come in a close second; kids and adults LOVE them.
If you need a recommendation, this muffin pan has held up well with very regular use.
Even More Muffin Recipes
- Blueberry Muffins
- Healthy Blueberry Banana Muffins
- Pumpkin Crumb Cake Muffins
- Zucchini Muffins
- Apple Cinnamon Muffins (with crumb topping)
- Bran Muffins
- Or try my all-in-one Muffin Recipe
Healthy Whole Wheat Apple Muffins
- Prep Time: 10 minutes
- Cook Time: 22 minutes
- Total Time: 35 minutes
- Yield: 12 muffins
- Category: Muffins
- Method: Baking
- Cuisine: American
Description
These simple and healthy whole wheat apple muffins come together quickly. Feel free to skip the optional nuts and make sure to use shredded apple instead of chopped apple.
Ingredients
- 2 cups (260g) whole wheat flourย (spooned & leveled)
- 1 teaspoon baking powder
- 1 teaspoon baking soda
- 2 teaspoons ground cinnamon
- 1/2 teaspoon ground allspice
- 1/2 teaspoon salt
- 2 large eggs, at room temperature
- 3/4 cup (180g) smooth unsweetened applesauce, at room temperature
- 2/3 cup (160ml) pure maple syrup, at room temperature
- 1/3 cup (70g) coconut oil, melted (or vegetable oil or melted butter)
- 1 and 1/2 teaspoons pure vanilla extract
- 2 cups (210g) shredded/grated apple (about 2 peeled apples)*
- optional: 3/4 cup (about 90g) chopped pecans or walnuts
- optional: 1 Tablespoon coarse sugar for sprinkling on top
Instructions
- Preheat oven to 425ยฐF (218ยฐC). Spray a 12-count muffin pan with nonstick spray or line with cupcake liners. Set aside.
- In a large bowl, whisk the flour, baking powder, baking soda, cinnamon, allspice, and salt together until combined. Set aside. In a medium bowl, whisk the eggs, applesauce, maple syrup, oil, and vanilla together until combined. Pour the wet ingredients into the dry ingredients, stir a few times, and then add the shredded apple and pecans/walnuts. With a silicone spatula, fold everything together gently just until combined. The batter will be very thick.
- Spoon the batter into liners, filling them all the way to the top. If using, sprinkle tops evenly with coarse sugar. Bake for 5 minutes at 425ยฐF, then, keeping the muffins in the oven, reduce the oven temperature to 350ยฐF (177ยฐC). Bake for an additional 16โ18 minutes or until a toothpick inserted in the center comes out clean. The total time these muffins take in the oven is about 21โ23 minutes. (For mini muffins, bake 11โ14 minutes at 350ยฐF (177ยฐC).)
- Allow the muffins to cool for 5 minutes in the muffin pan, and then transfer to a wire rack to continue cooling, or enjoy warm.
- Muffins stay fresh covered at room temperature for a few days, then transfer to the refrigerator for up to 1 week.
Notes
- Freezing Instructions:ย For longer storage, freeze the muffins for up to 3 months. Thaw overnight in the refrigerator, then heat up in the microwave if desired.
- Special Tools (affiliate links): 12-count Muffin Pan | Cupcake Liners | Glass Mixing Bowls | Whisk | Box Grater | Silicone Spatula | Cooling Rack
- Whole Wheat Flour: If you don’t have whole wheat flour, you can replace with the same amount of all-purpose flour. My team and I have not tested this recipe with gluten-free flour, but here are some gluten-free blueberry muffins you might enjoy instead. (Feel free to replace blueberries with chopped apple.)
- Maple Syrup: For best results, use pure maple syrup, not breakfast syrup. The darker the pure maple syrup, the stronger the flavor. So if your maple syrup is extra dark with robust flavor, slightly reduce to 1/2 cup (120ml). If your maple syrup is golden or light amber colored (not very dark), use 2/3 cup as instructed. You can substitute honey if needed, but reduce the honey to 1/2 cup (170g).
- Shredded vs. Chopped Apples: It’s best to use shredded/grated apples in this muffin recipe because they work as a wet ingredient. I do not recommend chopping them instead. Feel free to peel the apples before shredding or leave the peels onโdoesn’t matter either way.
- Why the initial high oven temperature?ย Like I do for mostย muffin recipes, bake the muffins for 5 minutes at a very hot temperature. Then, keeping the muffins in the oven, switch to a lower temperature for the remaining bake time. This initial high temperature will quickly lift the muffin tops so theyโre extra high, then the centers will bake during the lower temperature bake time. This trick makes beautiful bakery-style muffins every time.
- Nutrition Information: Using SparkRecipes calculator, these muffins come out to 195 calories, 7.5g fat, 30g carbs each.
Reader Comments and Reviews
Canโt wait to try! What can you use instead of apple sauce if you donโt have any?
Hi Clementine, applesauce is a pretty key ingredient in these muffins and we recommend sticking with the recipe as written for best results! You could try yogurt or pumpkin puree instead, but flavor and texture will vary.
All your recipes are wonderful.
My family and I love them.
I have 6 grandson ages 21 to 4 yrs old they love them too.
Thank you, Linda
These are fantastic! I substituted oat flour for the whole wheat flour and they are fantastic!!
These are fantastic! I substituted oat flour for the whole wheat flour and they are fantastic!!
Apples shooting out of our ears this yearโฆso so so many applesโฆOn the bright side, more reason to make delicious recipes like this one.
I just made ur whole wheat muffins how many calories per muffin??
Hi Miriam, see recipe Notes for nutrition information.
I have made this recipe several times before, and it is always good! I am out of maple syrup though, and I was wondering if I could possibly use molasses if I water it down a bit? Thanks!
Hi AB, Honey is our preferred substitute for the maple syrup. See recipe note. You can substitute honey if needed, but reduce the honey to 1/2 cup (170g).
These are absolutely amazing! I did make them with gluten free flour and they were perfect. Wonderful fall flavors and such a great treat
They are moist and flavorful. I used apples picked on the neighbour’s tree, with the peel. I added extra spices, similar to apple pie. It made 14 muffins.
Thank you for this recipe. We just moved to Germany and have a beautiful apple tree growing in our yard, so I wanted to do something with all the apples we picked (and we have to pick a lot of them to keep from going to waste)!
This healthy apple muffin recipe was the very first recipe we baked trying to learn our German oven, and thankfully it turned out just perfect. We’ll definitely be making a lot of muffins!
do you think i could add chopped apples in addition to the grated apples for more texture and apple goodness?
Sally, First I want to thank you for your website. I visit here often and always find the most delicious and succesful recipes. My trusty recipe go-to! Now on to these Apple muffins. I love them! I had Cassava flour in the pantry and never seem to find use for the flour so I just went for it… What can go wrong, right..? Well, success! 1 1/2 cups of the gluten free Cassava flour replacing 2 cups of whole wheat flour was perfect substitution. Texture came out fluffy and beautiful. I used chopped pecans as advised and topped with coconut sugar and pecan nut. Has anyone tried to add or replace spices with pumpkin spice? The flavors with cinnamon and all spice has yummy fall vibes and next time I just might take an other risk and see what pumpkin spice would do to join the party… Thank you, again!
I need to get rid of applesโฆcan I use homemade applesauce for this? I always just cook them with no sugar added- only cinnamon. Thank you so much!
Hi Tila, you can absolutely use homemade applesauce in this recipe!
My toddler adores these! Theyโre lightly sweet and they whip up fast so itโs a fun activity we can do together!
This muffins are alright. I appreciate that they are made without butter or sugar, but I find the quite bland. All the same, I am still grateful for a snack that I can feel good about eating! Thank you Sally
Hi Sally! Can I use pumpkin puree instead of apple sauce in this recipe?
Hi Simone, Applesauce is a pretty key ingredient here, but you could try replacing the applesauce with the same amount of pumpkin puree or mashed bananas, for a different flavor.
Just made these, and they are fantastic! Interesting fact: as I went to lower the temperature to 350, I notice the 2 eggs I forgot to add (on the counter.) Internet said to simply finish baking, and that the texture may be different (dryer, more dense, crumbly). Not the case here – they are perfect!
These muffins are delicious! The grated apples give this yummy flavor in every bite. I used melted butter as it was on hand though I will try with coconut oil next time. I have made other Sally’s muffin recipes and that 5 min @ 425 gives a fluffy top every time! Will make these again – the whole family loves them!
I made these with freshly milled flour and they are perfect!!! Moist and delicious, great flavor and texture. Saving this recipe for sure!
These came out great! I made a couple changes. I used. 1-1/2 cup of whole wheat flour and 1/2 cup of gluten free flour. Switched out applesauce for yogurt. And I only added 1/3 cup of packed brown sugar. I only had granny smith apples. They give out a lot of water when I was shredding them. So had to squeeze out of the juice. Overall it was softer than usual maybe due to the juice from apple. But tastes so good!
Can I make these mini instead? How should I adjust the baking time?
Thanks!
Hi Lindsay, for mini muffins, bake 11โ14 minutes at 350ยฐF (177ยฐC). Hope theyโre a hit!
Great muffins. We have an apple tree so there is plenty of apples. Love that the muffins are not too sweet. I will make these again and modify to use other fruit.
These were alright. Not my favorite though… They were really moist, but not quite the flavor and texture I was looking for.
Very excited to try this! Do you think raisins would work instead of nuts? Would you use the same amount?
Hi Michelle, yes! Same amount!