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.
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 and this muffin pan have both 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 (133g) 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 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 | Rubber 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.
Keywords: healthy apple muffins, whole wheat apple muffins
Made this today – as a loaf instead of muffins. Didn’t have enough apples, so I added dried cranberries in food processor with apples. Substituted pumpkin pie spice for allspice and walnuts for pecans, then added some apple juice to insure it was moist. Baked 45 minutes – turned out perfect!
★★★★★
Made these muffins exactly as written (amazing I had all the ingredients!). These are delicious! I thought they might be a bit heavy or dry due to the whole wheat flour but not so. Moist and tender. Just sweet enough with just a hint of maple flavour. Perfect for breakfast or mid morning snack. Thanks Sally for another great recipe…this is a keeper!
★★★★★
I made these because I thought I had apples that needed to be used up. After getting started, I found I only had 1 apple. Darn! I made up the difference with grated carrot and added in some currants. Excellent. (Oh, I also used all oil as I didn’t have applesauce.)
THank you for another great recipe.
★★★★★
This was a lovely recipe. I made some substitutions based on what I had at home but it still turned out great. Instead of maple, I used a mix of agave and honey. I didn’t have enough of either so I made sure the applesauce (homemade) was sweetened, by which I mean macerated in malibu and a teaspoon of coconut sugar. Also shredded apples and pears instead of just using apples.
I’ll be making this again for sure. Thank you
★★★★★
Wonderful muffins. I substituted 1 c of crushed pineapple for 1 c of shredded apples and it turned out great
I made these twice in one week! They are so tasty! One batch I just did shredded apples and the other I added chopped walnuts and used 1/2 C honey in place of the maple syrup. They are in the freezer for quick breakfasts! Thank you so much for the recipe.
★★★★★
Do you peel the apples before you grate them?
That’s up to– won’t make a difference in the recipe either way.
I made these this morning! They came out great. They almost tasted buttery despite being dairy free. I had purchased the wrong flour at the grocery store a few days ago (I got white all purpose flour with wheat germ instead of regular all purpose) so I figured this would be a good opportunity to use it. The only thing was that the muffins stuck to the liners. Not a big deal, but next time I will just grease the muffin pan so I don’t need cupcake liners at all.
★★★★★
These muffins are amazing!
★★★★★
Hi Sally,
What would you think about making this with carrots instead of apples?
Thanks for everything!
Carrots should work! Just be sure to shred your own large carrots and don’t use the bags of pre-shredded carrots sold in the store as they are much more dry.
These are so good! Not too sweet, nicely cinnamon-flavored, chock full of apples, and hearty without feeling stodgy. I used Honeycrisp apples, which I love for just about anything. I’m not normally a fan of nuts in baked goods, but I had some pecans so included them. They add a nice crunch. They turned out perfect, will definitely make again.
★★★★★
I made this for school breakfast meal prep for my daughter. Love them! So easy to make, not too sweet and they were a hit with the kids.
★★★★★
Hi Sally
Just made this recipe and subbed out one of the apples for grated carrots. Also, for the shredding/grating, I just blitzed everything in my Cuisinart. The muffins turned out DELICIOUS and you can hardly tell that they’re whole wheat. Thanks so much for sharing this recipe! I’m looking forward to using these to kick start my kid’s first week back in school. 🙂
★★★★★
How long should I bake these in a jumbo muffin tin?
Bake at 425°F for 5 minutes, then, keeping the muffins in the oven, reduce the oven temperature to 350°F (177°C) and continue to bake for 25-26 minutes until the tops are lightly golden brown and centers are set. Use a toothpick to test. Enjoy!
This recipe was super easy to follow and they came out great. Moist despite not having apple sauce and using wholewheat flour, this will now by my weekly mid-afternoon snack, thank you!
★★★★★
Sally, thank you for this delicious recipe. We just made them this morning. They came out great and the recipe is very forgiving. I don’t usually substitute in recipes but had no choice, and we really had a hankering for muffins but were running low on some ingredients. We ended up using a mix of walnuts/pecans, a mix of real maple syrup and honey, 1 tsp vanilla and 1 tsp orange extract, and 2 Macoun apples plus 1 red delicious (to get to 2 cups of grated apples.) It cleaned out my pantry (finished off all the ingredients listed above) so I must go to the supermarket now as I would like to make them again exactly as listed. 🙂 My kids and husband loved them and none of them realized they were whole wheat.
★★★★★
I made these for an as easy breakfast for my 13 month old. He loves them! Thank you!
★★★★★
Sally! These are the most amazing muffins I have ever made! I subbed cloves and nutmeg for the allspice and that made the flavor a bit off I think, but the texture and moisture are off the charts. Thank you! Will make again with actual allspice!
★★★★★
These are some of the best whole wheat muffins I’ve made to date. Moist and not overly dense like other recipes. Thank you! Planned on the banana ones you just posted until I mistakenly told my toddler about these, but they were definitely a hit. Another sally recipe to add to the permanent cookbook collection.
It’s been so long since I’ve made these, I forgot how good they are!! I made a batch this evening as I’m now 38 weeks pregnant and am trying to get a freezer stash together, it’s a little tricky because I don’t have a secondary freezer, just a small fridge one but I’m doing what I can, your freezer meal prep post has been super helpful! Thanks for that!
But ya about this recipe, I had a few pink lady’s to use up. I ran out of maple syrup, I only had about 1/3 cup so I used amber coconut nectar for the remainder and they turned out great! No loss of flavour I felt they would’ve had from honey. So leaving a couple out for myself but throwing most in the freezer! Also, I just wanted to let you know that these muffins aren’t in your healthy muffin category! I’m not sure if that was intentional or not but I feel like they should be there! I feel super not guilty when I eat more than one of these lol.
Hope everything is going great with baby Noelle!
I’ve made the Morning Glory Muffins in the past and was wondering if it would work to sub carrots for the grated apples in this recipe. I can imagine carrots and golden raisins would taste quite good in this base. I really love the sweetness level on these, especially as a snack for my toddler.
Marie– yes, absolutely. Carrots would be a great sub for the shredded apples.
These were delicious! I made a half recipe, used white whole wheat, and about half maple syrup and half molasses (b/c I didn’t have enough syrup!), which made them a lovely dark color and quite moist. I also used =amount of milk rather than applesauce, not having applesauce. Really perfect for the season!
I made this into a loaf—just out of the oven so haven’t sliced into it yet, but the batter tasted delicious and my whole kitchen smells amazing! Wonderful recipe for fall.
Amazing! These are so delicious and the perfect amount of sweet without sugar!!!!! Keeper recipe for apple season!! Thank you as always!
So delicious! I’m trying another double-batch after the family ate them up. The shredded apples are amazing, they kind of melt into the muffin and add flavour without being chunky.
My husband and kids don’t like bits of nuts in baked goods so I just added a bit of almond flour to up the protein and it worked just great! thanks!
Made these yesterday. Really really good – thanks for an awesome recipe!
Amazing!! Super moist and flavorful. Thanks for the great recipe!
Hey Sally, is there anyway to make this recipe into a loaf instead??
Yep! This batter will fit into a 9×5 pan. Bake at 350F. Unsure of the exact bake time.
Love, love these muffins!
I’m not sure how many times I’ve baked these. I love that this is a no-sugar recipe, and that you use whole wheat. I use all non-GMO and organic ingredients and cut maple syrup to 1/2 cup 😉 Thank you for sharing such a great recipe! My husband is a Marine, and he asked me to bake these for his Marines 🙂
Hi, Sally. If I use Whole White Wheat flour would I need to change the ratio?
No need to change anything besides the simple substitution!
Sally these are delicious! I made them using half whole wheat flour and half white flour. Oh and they were plenty sweet, I really didn’t notice any difference in sweetness versus using sugar instead of maple syrup. Sooooo good!!!!!