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
These look delicious. Wondering if I could mix a little refined sugar with the syrup and use less? Maple syrup is very expensive where I live – it would be $0.10 for sugar but $2.50 for 1/2c maple syrup. So I thought I could still get the benefit of the syrup but more like a reduced sugar muffin??
Hi Opal, we haven’t tested it but would love to know how they turn out if you give it a try!
I am making this today. Muffins are my favorite breakfast food. Plus, I can make extra and freeze them.
I am trying to do holiday baking early because I need to have arm surgery in December. I would like to see more recipes that are good for baking ahead.
Hi Brenda, hope you enjoy these muffins! We try to include make-ahead instructions for any recipes that can be made or prepped ahead of time. Be sure to see the recipe notes! If you want to get a head start on cookie making, this How to Freeze Cookie Dough (Video) post might be helpful!
What can I use in place of coconut oil? Allergies.
Hi Peggy, you can use melted butter or vegetable oil instead. Hope you enjoy the muffins!
Tasted great, WW Flour didn’t make it taste “too healthy” per the family. I substituted olive oil for coconut oil. Loved the first baking at higher temp, it really did make muffin tops rise fast and stay high and looked great!!
Could you add peanut butter to these for some extra protein? Thanks!
Hi Stephanie, we haven’t tested anything and it would likely take some tweaking of the other ingredients. You could always add some melted peanut butter to the tops of the baked muffins. Let us know what you try!
Looks great! Can I only use grated apples instead of apple sauce + apples?
Hi Emilie, we don’t recommend leaving out the applesauce. It’s key for moisture.
What a great recipe! Thank you for sharing! I modified a little I used only 1/2 c maple syrup and added pecans and soaked raisins. I did a few splashes of almond milk to make up for the loss of liquid by using less maple syrup. So yummy!
I’m glad I tried this recipe! I wanted something without sugar and butter and this hit the mark! They are so moist and flavorful with the cinnamon and allspice not to mention apples AND applesauce (sugarless). Thanks for this great recipe that I’ll use over and over.
Super Yummy! I only had regular all-purpose flour on hand so I used that instead with no changes to recipe and came out perfect, though not as healthy without the whole wheat.
Can I use gluten free flour in this recipe?
Hi Chris, We haven’t tested this recipe with gluten free flours, but some readers have reported success using 1:1 flour substitutes (like Cup4Cup). If you try it, let us know how it goes!
This recipe is great! I used monk fruit sweetener in place of maple syrup (1:1) and it worked perfectly!
I made these today and was very impressed. I am trying to make some healthier choices with my eating (I typically bake with a lot of refined sugar and butter). Although they aren’t as sweet as I thought they would be, they will be a delightful snack during the day. Thank you for sharing!!
I would love to make these, can u tell me a substitute for eggs in this.
Hi Meghna, we haven’t tested this recipe with any egg substitutes, but let us know if you try anything.
What are the nutrition facts for 1 muffin? I don’t see them on here.
Hi Kayla, We don’t usually include nutrition information as it can vary between different brands of the same ingredients. Plus, many recipes have ingredient substitutions or optional ingredients listed. However, there are many handy online calculators where you can plug in and customize your exact ingredients/brands. Readers have found this one especially helpful: https://www.verywellfit.com/recipe-nutrition-analyzer-4157076
Made these this morning and they came out so well! I didn’t add any nuts to mine because I like my muffins soft without a crunch. I might try adding nutmeg or more cinnamon to the next batch to give it an even warmer taste to them. Definitely adding this to my muffin rotation! They’re so easy to make.
I made these yesterday, they turned our very very dense.. I followed the recipe to the T, yet it turned out super dense.. how can I make it lighter
Hi Sonea, was the batter over mixed by chance? That can cause muffins to bake up squat and dense. These are a bit denser than, say, blueberry muffins, but being careful not to over mix the batter will help. The whole wheat flour lends a heartier texture, too. Thanks for giving these a try!
These muffins were delicious as is. Could chunks of apples be added in addition to the grated apples? I like to have chunks of apples in my muffins. Thanks!
I made these with chopped, cooked apples (4) as I did have any applesauce. So the apples were soft, the muffins look and taste great. If you try just chopping without cooking just make them smallish chunks. Enjoy!
I’ve made this recipe twice and love it. I would like to reduce the sugar though. From just the 2/3c maple syrup, I’m calculating this at 12grams of sugar per muffin. Can I just reduce the amount of maple syrup? Or should I replace with water for moisture?
Hi Denise, I haven’t tried reducing the sugar and I do fear the muffins may taste dry. You can try replacing with water. Let me know how the batch turns out.
Oh my goodness. I can’t rate this recipe yet because I made a big mistake and I don’t know they will turn out. I forgot the coconut oil that I had melted in the microwave. The batter tasted delicious, the tops did rise, they smell good, but we shall see. What a dumb thing to do!
I love all your recipses… I would hope going forward you can start adding the sugar content in your nutritional facts. J
Hi Bridgette, We don’t usually include nutrition information as it can vary between different brands of the same ingredients. Plus, many recipes have ingredient substitutions or optional ingredients listed. However, there are many handy online calculators where you can plug in and customize your exact ingredients/brands. Readers have found this one especially helpful: https://www.verywellfit.com/recipe-nutrition-analyzer-4157076
Sally, I love this recipe. How can I make it as a cake, 13 x 9 pan or two layer cake please?
Hi Darlene, here’s everything you need to know about cake pan sizes and conversions. Or, here is our apple cake recipe instead!
Thank you so much. The muffins are amazing and I wanted to take it in cake form to a card party gathering…
How would you adjust time for mini muffins…sometimes easier for kids?
Hi Chris, for mini muffins, bake 11–14 minutes at 350°F (177°C). Hope they’re a hit!
Hi Sally,
I love your recipes and I have made a number of them and they always turn out fantastic. Can I substitute whole wheat pastry flour for whole wheat flour? Thank you ; )
– Veronica
Hi Veronica, that should be fine for this recipe. Enjoy!
Yum! I didn’t have apple sauce, so Inused Greek yogurt. This is a keeper – thanks!
I made these yesterday and they are delicious. Sweet, moist and no sugar! I’ll definitely make these again!
These are delicious! I will definitely be making them again.
Best apple muffins I’ve tried and my children love them too!
Can I freeze these?
Hi Amy, absolutely, see recipe Notes for full freezing instructions.
Can this be made into loaves?
Hi Bridget, absolutely. This batter will fit in one 9×5-inch loaf pan. You can bake at 350 degrees, but we’re unsure of the exact bake time. Keep a close eye on it and use a toothpick to test for doneness. Enjoy!
I cannot wait to try these! I have white whole wheat flour, would that be ok to use or would it change the texture?
Hi Christine, you can absolutely use the white whole wheat flour here—same amount. Enjoy!