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. ★★★★★“
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 aren’t weighed down with fat.
Here’s Why You’ll Love These Healthy Apple Muffins
- Quick and easy
- No mixer required
- Zero refined sugar—use 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 5–10 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 it—use 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 flour (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 425°F (218°C). 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 425°F, then, keeping the muffins in the oven, reduce the oven temperature to 350°F (177°C). Bake for an additional 16–18 minutes or until a toothpick inserted in the center comes out clean. The total time these muffins take in the oven is about 21–23 minutes. (For mini muffins, bake 11–14 minutes at 350°F (177°C).)
- 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: 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 on—doesn’t matter either way.
- Why the initial high oven temperature? Like I do for most 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 they’re 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
Absolutely top-notch recipe!! So delicious and light!! The baking method with high heat was spot on for nice, tall muffins. Thank you, thank you, thank you!!!!
Can’t wait to try these, hoping to make them tonight. The only whole wheat flour I have is pastry whole wheat flour… would that work? Can I substitute all purpose flour? Thank you so much!
Hi Karly, Whole wheat pastry flour is finer and has a lower protein content. I would look it up online for a more in-depth look at the differences. You could use either in this recipe.
Hi, I would love to try this recipe out. One thing, I am not a huge fan of cinnamon, would it still work if i cut it out?
Hi Sara! The flavor may be a little lacking without cinnamon – even just 1/2 tsp instead of 2 tsp would be good. You could also add 1 tsp cardamom or ginger (if you like those flavors) here, too. Let us know what you try!
Hi Sally,
Made these this morning and have to say not overly keen on the allspice. I have a pretty good idea for its use, to mask the whole wheat flour bite. Next time I make these I am going to sub out some of the w/w flour with w/w pastry flour which has a lot less bite.
Deb
Do you think I could add a crumble to the top?
H Lily, you definitely could. Try the crumb topping included in this apple cinnamon crumb muffins recipe.
These are great. I used just one cup of whole wheat flour, and added 1/2c. whole wheat einkorn flour and 1/2c. millet flour. So good!
The first time I made this recipe I omitted the nuts (school doesn’t allow them) and my son liked them but they didn’t have enough apple flavour and were a little bland. So this time instead of nuts I added small, cut up apple pieces in the same amount as the nuts would have been. It is markedly better. (Used honeycrisp in case anyone is curious.) I will be baking it this way moving forward. It was dense but that is fine for a hearty autumnal muffin.
Delicious, moist texture, healthful…all in one muffin. Next time I will cut back on the raisins and add the addition of chopped walnuts.
Hi I love this recipe!!
I have a question though… could I use self raising whole meal flour? And if so what would the process be? Ie. Omit bicarb?
Hi Jess, we don’t recommend using self raising flour. They contain different amounts of leavening and it would require some recipe testing to properly incorporate.
Hi Sally, with the large amount of applesauce in this recipe, do the muffins end up with a spongy texture? thanks for letting me know, they sound delicious!
Amazing recipe! This is by far my favorite muffin recipe to date. It was easy to make, healthy, flavorful, and moist. When the muffins are heated the cupcake liners also come off easily, which is a nice perk of this recipe, as it’s something I’ve had trouble with other muffin recipes in the past. Definitely will make this again!
A miss. I followed the recipe and instructions exactly. The batter was extremely thick and dry looking but she did say that it would be thick so I didn’t think too much of it. My husband said they were dry, gritty, and didn’t have much flavor.
I just made this recipe, and oh my god it’s SO GOOD!!! The flavor is just outstanding, and it comes together so easily.
However, I have to admit that I did make one major change to the recipe. I’ve been trying to find a good recipe for higher protein baked goods, and was getting pretty disappointed every time. Sally has never let me down before with flavors, so I decided to take a chance and sub half of the flour for protein powder (130 g of each, I used orgain vanilla flavor pea protein powder). Otherwise, I followed the recipe almost exactly. I did use AP flour in lieu of whole wheat since that’s all I keep in the house. For the oil, I used vegetable oil; for the apples, I ended up slightly over (222 g) but figured the extra wetness would help the protein powder side of things.
Even with the high content of protein powder, the batter came out exactly as described (very thick) and the crumb baked beautifully, just like a normal muffin. Other protein powder recipes have left me with a crumbly or stodgy mess, and this was perfect. For anyone else trying to find a good recipe for higher protein baked goods, look no further!!! This is THE one.
(With my ingredients, the nutrition per muffin comes out to 155 cals, 7 g protein, 8 g fat, 17 g carbs.)
With all due respect, you did not make this recipe. You can’t change all the ingredients and say you made the recipe.
I too like high protein options, so I appreciate you sharing your experiment and results. Trying variations and reporting positive results IS making the recipe and helpful for those with similar tastes. Thanks.
These are amazing! They are so moist for whole wheat muffins, and full of flavour. I had to make my own applesauce, and I used honey instead of maple syrup, and they are perfect!
Wow, very pleasantly surprised how good these turned out… was skeptical… most whole wheat muffin recipes are just too dense and blah. Followed the recipe exactly, with pecans, and also threw in 3/4’s cup of blueberries (were going wrinkly and no one was going to eat them). Turned out fantastic! Thanks for a healthier muffin recipe that actually tastes good!
These muffins are so delicious! I was pleasantly surprised at how moist they are. I know the recipe says they’re supposed to be, but they really are! Haha. And it’s just the right amount of sweetness. Not overly sweet, but enough to keep the taste buds happy. Thank you so much for the recipe!
Great muffins, but I have a question. The shredded apples were VERY wet, should I squeeze out the excess liquid or use it in the recipe. THANKS.
Hi Millie! If they seem extra wet, you can give them a quick squeeze/dab.
I love the way the muffins rise. The coconut oil gives it a lighter texture.
These turned out so well! I have made them twice, once with liquid measures and once with weight and it turned out perfect both times. My only suggestion is to keep the apple shreds short if you’re trying to get them to distribute evenly throughout the muffin.
These are fabulous! I followed the recipe (but was too last minute to have eggs etc at room temp). The muffins are sublime
Recipe is good starting point. Nice flavor and texture. Only issues for me were are a tad too much maple syrup and need to cut cinnamon back to 1 1/2 teaspoons and allspice to 1/2 teaspoon. Now it’s time for me to start making substitutions for grains. I’m thinking WW flour, oats, and almond flour. Great recipe if you’re seeking a healthier option.
Applesauce isn’t always readily available for me. Is there something I could substitute this with? Or could I simply puree another apple?
Hi AT, you could substitute some of the applesauce with plain yogurt, but we wouldn’t swap all of it. You’ll lose a lot of flavor. We’d recommend waiting until you have some applesauce on hand, or using your apples to make some!
This is a great recipe! I actually didn’t have applesauce on hand and had some crushed pineapple (unsweetened) left over from carrot cake so used that and it worked fine, didn’t overshadow the apple at all. I did strain the crushed pineapple a bit so that it wouldn’t add too much liquid.
Appx how many mini muffins does this make..Guessing 36ish? I use USA MADE MINI PANS
Hi GMJ, we’re unsure exactly how many mini muffins this would make. Let us know if you try!
Loved these and all the wholesome ingredients. The end result was worth the extra step of shredding the apples. Only change I made was adding some nutmeg. Terrific recipe.
IF I wanted to add in ” some” soaked & drained” raisens ( along with the optional chopped walnuts[ 1/2 ish cup] how much rainsif any could be added ?
Hi GMJ, we’d keep the total amount of add-ins about the same, so you could use a combination of raisins and nuts of about 3/4 cup.
I made these to go with a ham and bean soup and they were the perfect compliment. My husband loved them. I didn’t have any applesauce but I did have an old banana in the freezer so I thawed and mashed that up and it worked just fine.
These are delicious!! So much flavor, super moist, and no guilt 🙂 I actually got 15 muffins from this recipe– yay!
Thanks so much Sally!
Is it ok to use nondairy yogurt/ pudding instead of the apple sauce, or rice milk? Many thanks
Hi Brindy, you could substitute some of the applesauce with plain yogurt, but we wouldn’t swap all of it. You’ll lose a lot of flavor.
I had several apples that were grainy and not crunchy so this was the best recipe. The muffins came out delicious. It’s hard to believe they are healthy with the maple syrup and coconut oil.
Thank you Sandra! I just asked that question. I have several apples that are on their way out and wondered if they’d work.
Hi Ellen, in general, softer apples should be avoided when baking. In this particular recipe, you’ll want to make sure they aren’t too soft that they turn mushy when trying to grate them. Let us know if you give the muffins a try!
Hi! I’m super excited to bake these muffins for my toddlers. I was wondering if the cooking time would be the same if I used a mini muffin pan instead? I’m new to the baking scene. Thanks!
Hi Chelsea, for mini muffins, bake 11–14 minutes at 350°F (177°C). Hope they’re a hit!
Thank you so much. Apparently I missed that when I read through the recipe the first time haha. They turned out delicious and my one year old loves them!