Whole Wheat Apple Cinnamon Muffins

Hearty, healthy, and satisfying whole wheat muffins filled with sweet apples and plenty of cinnamon spice!

whole wheat apple cinnamon muffins

With zero refined sugar, by the way. (!!!)

Yep, I went there. The streak of healthy goodness continues. And guess what? Kevin loved these muffins. Not for one little second realizing that hello… they’re (1) whole wheat, (2) filled with fruit, and (3) not with sugar.

But before I get to the muffins: is it just me or did this week crawl by at a turtle’s pace? Scratch that. More like a snail. Whatever its speed, let’s just all be thankful that the weekend is here and it’s time to warm up and lounge around with healthy apple cinnamon muffins on our plates.

Cold weather necessity right here! ↓

overhead image of whole wheat apple cinnamon muffins

As you’re probably aware, I don’t mess around when it comes to muffins. Especially when it comes to muffins of the healthy variety. Chocolate banana resembling brownies (seriously, have you tried them?), strawberry chocolate chip with shockingly low calorie count, and these skinny banana blueberry muffins that gain all sorts of buzz this time of year. Lightened-up muffins are the peanut butter to my jelly. Sprinkles to my birthday cake. Netflix marathons to my weekends. In short: I can’t live without ’em.

So let me show you a new way to make them, apple cinnamon style.

Today’s muffins are adapted from my simple morning glory muffins, which have all sorts of goodies packed inside like grated apple, grated carrot, raisins, nuts, etc. Thick: carrot cake, but lightened-up. For today’s apple cinnamon 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 oil. This way the muffins keep their moist, rich texture but aren’t weighed down with fat. Sometimes I find that replacing all of the fat in muffin recipes results in a rubbery texture. I use melted coconut oil in these, but you can use canola or vegetable instead.

2 images of muffin batter in a glass bowl and muffin batter in a muffin pan

Other healthy superstars: whole wheat flour (yes to that!) and apples. The muffins get a lot of their flavor and sweetness from the grated apples, so I suggest using a sweeter variety. And, of course, a variety you love because you’ll taste a lot of apple. I use Pink Lady or Fuji.

Also inside: pure maple syrup. None of that breakfast syrup stuff! The real deal, for concentrated flavor. Maple syrup in muffins is my new thing. It replaces the need for refined sugar. They aren’t super sweet muffins so if you love the high sugar stuff, you’ll miss the sugar here. A lot of sweetness comes from the apple, so again– that’s why I urge you to use a sweeter variety.

We’ve also got lots of cinnamon, some allspice, and chopped pecans for all sorts of delicious spice and goodness.

whole wheat apple cinnamon muffins in a muffin pan

You know how whole wheat muffins taste completely uninteresting? You don’t even want to waste your time. Or your calories. That’s not the story here. With all those sweet apple pieces overflowing every bite, the purely magical maple syrup lingering, that robust allspice, the cinnamon swirling, and fat-cutting applesauce… there’s so much to love. In every single warm, snuggly, healthy, unrefined sugary, whole wheat bite. ♥ I just described these as snuggly. And I’m OK with that.

whole wheat apple cinnamon muffins

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3 images of whole wheat apple cinnamon muffins

Whole Wheat Apple Cinnamon Muffins

  • Author: Sally
  • Prep Time: 15 minutes
  • Cook Time: 24 minutes
  • Total Time: 40 minutes
  • Yield: 15 muffins
  • Category: Muffins
  • Method: Baking
  • Cuisine: American


These healthy, simple, and amazing whole wheat apple cinnamon muffins are made without refined sugar.


  • 2 cups (245g) whole wheat flour* (spoon & leveled)
  • 1 teaspoon baking soda
  • 1 teaspoon baking powder
  • 2 teaspoons ground cinnamon
  • 1/2 teaspoon allspice
  • 1/2 teaspoon salt
  • 1/2 cup (64g) chopped pecans*
  • 3 large eggs
  • 2/3 cup (160ml) pure maple syrup (not breakfast syrup, the real stuff)*
  • 1/3 cup (80ml) vegetable, canola oil, or melted coconut oil
  • 1/3 cup (60g) smooth unsweetened applesauce*
  • 1 and 1/2 teaspoons pure vanilla extract
  • 2 cups (240g) shredded/grated apple (about 2 apples)*


  1. Preheat oven to 425°F (218°C)6. Spray a 12-count muffin pan with nonstick spray or use cupcake liners. This recipe makes 15 muffins, so prepare a second muffin pan with 3 liners.
  2. In a large bowl, whisk the flour, baking soda, baking powder, cinnamon, allspice, salt, and pecans together until combined. Set aside. In a medium bowl, whisk the eggs, maple syrup, oil, applesauce, and vanilla together until combined. Pour the wet ingredients into the dry ingredients, stir a few times, then add the grated apple. Fold everything together gently just until combined and no flour pockets remain.
  3. Spoon the batter into liners, filling them all the way to the top. Bake for 5 minutes at 425 then, keeping the muffins in the oven, reduce the oven temperature to 350°F (177°C). Bake for an additional 18 minutes or until a toothpick inserted in the center comes out clean. The total time these muffins take in the oven is about 23-24 minutes, give or take. (For mini muffins, bake 11-14 minutes at 350°F (177°C).) Allow the muffins to cool for 5 minutes in the muffin pan, then transfer to a wire rack to continue cooling.
  4. Muffins stay fresh covered at room temperature for a few days, then transfer to the fridge for up to 1 week.


  1. Freezing Instructions: For longer storage, freeze muffins for up to 3 months. Allow to thaw overnight in the refrigerator, then bring to room temperature or warm up in the microwave if desired.
  2. Flour: 2 cups of white whole wheat, whole wheat pastry flour, or all-purpose flour work too.
  3. Pecans: Instead of pecans, try chopped walnuts or even sunflower seeds. Or leave out completely. If using the nuts, feel free to toast them for 10 minutes at 300°F (148°C).
  4. Sweetener: You can use honey for the maple syrup, but the flavor will be different. Maple works so well with the apple cinnamon!
  5. Applesauce: Instead of applesauce, use an extra 1/3 cup of oil.
  6. Apples: Use a sweeter variety of apple that you love. I’ve used Pink Lady and Fuji. Both fantastic in these.
  7. Why the Initial High Temperature? The hot burst of air will spring up the top of the muffin quickly, then the inside of the muffin can bake for the remainder of the time. This helps the muffins rise nice and tall.
  8. Nutrition Information: Using SparkRecipes calculator, these muffins come out to 184 calories, 8g fat, 25g carbs each.
  9. Adapted from Simple Morning Glory Muffins.

Keywords: apple cinnamon muffins, whole wheat apple muffins


Comments are closed.

  1. Heather (Delicious Not Gorgeous) says:

    i love muffins on the less sweet side- most of the time i eat them for breakfast or snack, when i try to limit the amount of sugar i eat (plus my taste buds just prefer less sweet things in general). and love the double apple action! the more apple the better (:

    1. Laura ~ Raise Your Garden says:

      Totally on board with less sweet things! Use Xylitol in place of sugar and it works really well! Hard to substitute for baking though……you can use half and half but not all because the texture doesn’t come out quite the same. And odd as this sounds ~ my New Year’s Resolution is to eat more treats this year and not be so hard on myself! Weird. I know! =) 

      1. Same! I am right there with you. I have been so hard on myself about calorie counting for the past year. I am happy with my weight, but try extremely hard to maintain it. I am now trying to learn intuitive eating and enjoy what I want!

      2. Laura, I never have limits on what I “allow” myself. I find that when I do, I crave it more!

    2. Just had to make these today. I used the 2 apples I had left in the fridge not sure what type but they are quite tasty.  I wish I wasn’t so obsessed with baking because I can’t control myself, Thank goodness my hubby will eat everything I cook and bake or I’d be in big caloric trouble. Have you ever cooked with Truvia? I tried making meringue cookies the other day with Truvia and the whites wouldn’t beat correctly any idea why?

      1. I never recommend sugar subs in baking, especially finicky super particular recipes like meringue.

  2. Pure maple syrup is crack. Can’t resist it in plain form, can’t resist it in maple candy, and sure can’t resist it in muffins. Perfect breakfast!

    1. Girl, me either!! Haha! I was in heaven when we went on our honeymoon in Montreal! Maple candy, maple tea, etc etc etc! We even went to this shop Les Delices de l’Erable that poured maple syrup onto a chunk of ice and then rolled it onto a stick as a lollipop! They even had the museum of maple there haha 

      So yes, now I want to try these maple apple muffins!!!

    2. OMG maple candy. 🙂

  3. I’m assuming honey in place of maple syrup would be okay? Have you tried it?

    1. I have– see my recipe note!

  4. Laura @ The Bluenose Baker says:

    I will be making these this weekend! I’ve been on the hunt for a tasty, healthy apple muffin recipe for a while. None of them have quite measured up, but I have high hopes for yours!

    1. Let me know how you like them, Laura!

  5. Yes! These are a perfect recipe to make for snacking on all through the month! I love that you’ve made them with whole wheat because that always makes it easier to eat a whole dozen and not feel as guilty!

  6. These look amazing! Pinned 😀
    Can i use honey instead of maple syrup?

    1. Yep, see my recipe note.

      1. Thanks!
        Also, where do you get your colored distressed wood backgrounds for photos? did you make them? they look so amazing!

      2. I get a lot of them from here: http://ericksonwoodworks.com

  7. Priya Krishnamoorthy says:

    Can I use honey instead of maple syrup? 

    1. Yep, see my recipe note.

  8. Leah @ Grain Changer says:

    Gahhhh, I am so excited to try these (gfree, of course!) All of your skinny muffins are my go-tos, and Anthony is a super-fan of them as well. Keep ’em coming!!! 

  9. Madeline @ Teen's Tasty Eats says:

    These muffins sound  so incredibly fantastic!! I love my healthy muffins, and adding apple and cinnamon? Whoa. One question: Do you think I could replace the oil with more applesauce or banana? Thanks!

    – Madeline<3

    1. Madeline, I note that in the post. I find they taste quite rubbery without the fat from oil. I don’t recommend it!

      1. Madeline @ Teen's Tasty Eats says:

        Ok thanks Sally!! I definitely use oil when I make them!!!

        – Madeline<3

  10. I’m on the couch, still in my PJs, desperately wishing you also had a food delivery service. How I wish some of these would just appear! They sound/look amazing!

  11. Looks and sounds yummy Sally! Thanks for the inspiration as I definitely need to be on the healthy bandwagon now. 

  12. These muffins look right up my alley! I love any and all things apple cinnamon, and this time of year, of course, I’m trying to eat a little bit healthier — but I don’t want to give up baking! I made a whole wheat blueberry coffee cake for breakfast this past Sunday; this weekend I’ll give these muffins a shot and perhaps some healthy bran muffins too. Hope your January is well 😉 

  13. Sounds good. Thank you and have a great weekend.

  14. [email protected] Cooking with a Wallflower says:

    Oh my god! These apple muffins look so delish! I can imagine myself waking up to these everyday!

  15. Angela @ Witty Aspirations says:

    This sounds amazing!  We’ll be trying it this weekend 🙂  Thanks for sharing.

  16. I love these! I’m so making these for breakfast for the following week. 

  17. Hi Sally, 

    Just wondering do you mean “spray the muffin paper cups with non-stick spray?”  I have never heard of that before – – – but if it works, I love it!!!    Thanks
    Also, I want to say, that not only do I look forward to your recipes, but also your photo’s are simply fabulous!

    1. Thanks Noel! That is not a direction in these muffins- I direct to spray the muffin pan directly with a nonstick cooking spray (like Pam) or use paper liners. You do not have to spray the paper liners.

    2. Actually the recipe does indeed say that. I noticed that too right off the bat. “Spray a 12-count muffin pan with nonstick spray or use greased/sprayed cupcake liners.” I used my non-stick muffin tins and they came out beautifully.

      1. Thanks Karen, I missed it! There is no need to spray the liners.

  18. Lisan, you’d have to use more baking powder. And I’m unsure of the exact amount without testing it myself. How about you try these muffins instead? You can sub in chunks of apple for the blueberries and add another teaspoon of ground cinnamon.

    1. Thank you so much! I will probably try both recipes and just experiment with the baking powder in these. The blueberry ones also look delicious!

  19. How sweet would you say these taste? I’m asking because I would like to make them for my Mom and she likes her muffins just barely sweet so i would like to know if I should reduce the maple syrup when making them for her. Thanks in advance!

    1. Feel free to reduce the maple syrup. There is still some sweetness, of course, but if she prefers muffins without much sweetness at all– I would reduce. Though they may taste a little bland.

  20. Natasha @ Salt and Lavender says:

    These would make the perfect at-my-desk breakfast. Yum!!

  21. Perfect for this weekend! 

  22. Anna @ Crunchy Creamy Sweet says:

    My kids love muffins and the whole wheat versions so I need to make a batch of these beauties! Pinned! 

  23. I’ve been binging on decadent cakes and things for the past month, so this is a great recipe to start the year with. Quick question though, could I make a third of this? I usually have decent success halving muffin recipes, but since this needs three eggs, I’m thinking just dividing everything by three would work. Since you have weights for everything, it should be reasonably easy (started using my scale recently thanks to your suggestion, and I’m never going back to volume. I don’t think I know where my measuring cups are!). Thoughts?

    1. I think making 1/3 of this recipe would work, but you run a risk with the baking soda. That never seems to cut down properly yielding the same taste, texture, and rise. Let me know if you try it!

  24. I love muffins that are not too sweet! Instead of Maple syrup, I will try these with light Agave.
    I use Agave in coconut flour pancakes, and a few other recipes. 

  25. I made these this afternoon. I am on Day 10 of a year without refined sugar. 355 to go. This recipe came at the perfect time. They are indeed less sweet than normal muffins but I think our tastes need to be re-refined anyway. They’re really good.

  26. These look delish! And healthy too?! Can’t get much better than that!
    Thanks for this recipe Sally 🙂

  27. No joke, I got home and saw this and I said out loud,
    “I want to make these right now.” And I did. And they’re delicious. I used another 1/3 cup of oil (I used extra light olive oil) because I didn’t have any apple sauce. They’re so light and airy and warm I love it!

  28. I made these muffins last night and just had one for breakfast this am. They are so moist and delicious and the best part is no refined sugar! Thank you Sally for your recipes that never fail to please!!!!

  29. I just made these ans they are great!  Everyone loves them.  Very, very good!!!  It is cold here in Kansas and these along with a pot of soup is supper tonight and leftovers!  Thank you!

  30. Another terrific recipe, Sally, as always – these will be my Monday’s saving grace.
    Quick question before I get to work: do you think subbing the applesauce with greek yoghurt might work too?

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