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


  1. These were great,  I made a couple of changes, I made my own applesauce and used about 400gr.instead of 60gr.  I also mashed a small not too ripe banana for sweetness,  and it did the trick, could barely taste the banana wich is a plus for me since I’m not a big fan of cooked banana taste. These were sticky on the outside and cakey but moist on the inside. also used honey. 

  2. 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!

  3. Anju Anto Sunil says:

    Can I use butter instead of oil? If yes what would be the difference it makes in the muffins??

    1. I would use melted butter. The muffins may not be quite as moist, but still very tasty.

  4. Hey! If I leave out the pecans should I change anything else?

  5. Can avocado or olive oil be used instead of vegetable oil?

  6. I would assume coconut flour could be used in place of whole wheat flour? Thanks! These look delicious!
    I look forward to trying them out!

    1. I haven’t tried it.

  7. Thank you so much for sharing this wonderful recipe! I have been fighting  migraines and have been trying to eliminate processed sugar from my diet as something I have heard can help. However, I have a definite sweet tooth, so that is hard for me, but these muffins have been just the ticket. Lightly sweet- they help immensely with the sweet tooth cravings. My kids gobble them up too- they’re a new family favorite and are getting made weekly around here. Thanks again!

  8. Thanks for the feedback, Elaine! Making this as a loaf sounds delicious!

  9. Hi Sally,

    I was very excited to try your muffins but was disappointed that you don’t give calorie count??

  10. Hi Sally,
    I adore this recipe! I see you have a master muffin recipe on the blog, but was wondering if I could do the same with this “healthier” (sugar free) recipe. How would I make a blueberry, carrot, banana etc. muffin using this recipe? Would it work?
    Thanks for all your amazing recipes!

    1. Hi Mandy! A lot of my healthier muffin recipes are similar– a little different from this one. But you can take any of these and use your favorite add-ins!

  11. My daughter loved these muffins when I made them a few months ago with the exception of the grated apple. She’s not a fan of apple texture in general. Can I put the apple in the food processor and purée it instead of grating? 

    1. I don’t recommend that as it would be too much liquid, though you could puree about half of it instead.

      1. That’s what I was worried about. Thanks! 

  12. What is the difference in time If I’m using large muffin tins? Making several small muffins as opposed to several large ones will leave my family wanting more, and unless I make a double batch (which will probably happen anyway) we won’t have any left over (which would be nice to be able to take these to work).

    1. So usually I bake jumbo muffins for 5 minutes at 425, then lower the temp to 350F for an additional 20-23 minutes or until cooked through!

  13. I want to make this in a bread pan, do you think it would turn out ok?

    1. Definitely! I’m unsure about the bake time. Bake at 350F.

  14. Jennifer Shirazi says:


    I am thinking of making these as mini muffins to put in my 3 year old’s lunch box. Any ideas about cooking time and temps? Thanks!

    1. See the recipe (step 3) for mini muffins.

  15. 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. 

    1. Marie– yes, absolutely. Carrots would be a great sub for the shredded apples.

  16. Hi, I just came across this recipe and I wanted to make these for my sons preschool class. But I will be using a mini muffin pan. Should I still bake at the high temp, and for how long do you think? 

    1. See step 3 🙂 For mini muffins, bake 11-13 minutes at 350°F (177°C). — no initial high temp

  17. 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! 

  18. Do you know if the “pop up” method with the hot temp will work with gf muffins? I have a banana recipe that’s kinda similar to this but with almond flour and brown rice flour and I’d love them to be raised like how these turned out. 

    1. I’m unsure without testing the recipe out myself, sorry!

  19. Sally,
    I am so thankful for you. You are absolutely amazing at what
    you do. I have begun using your recipes and have gotten rave
    reviews from my husband without even discussing where the
    recipe came from, meaning there is no bias. I made your whole
    wheat pancake recipe yesterday (using sprouted wheat flour),
    for my family of seven and we absolutely enjoyed them as they
    were light and delicious.

    Your whole wheat flour recipes are right on. Your addition
    of fats, such as coconut oil and milk products, such as
    yogurt and sour cream are just what whole wheat flour needs to
    be rich and moist. It is also what the body needs to be healthy
    and strong. I don’t know if you have studied this from a health
    perspective, but on two fronts you have touched base with
    Well, I wanted to ask you, have you tried sprouted wheat flour?
    It is exceptional. Regular whole wheat flour has high nutrient
    potential as we know. Yet, all those nutrients are not readily
    available for assimilation by the body, unless it is first sprouted.
    In addition, sprouting makes it so much more delicious as the
    sugars contained within the seed are also released through this

    The whole wheat kernel is a seed. Through the process of sprouting,
    seeds release their nutrients and sugars for use for the new plant to
    grow. The plant uses the nutrients to be healthy, and uses the sugars
    for energy in the growing process, just like our bodies. When seeds
    are sprouted and then dried and ground into flour, those same
    nutrients and sugars that were available for the seed to grow into
    a new plant are now available to our bodies for high assimilation.
    Did I also mention they are made delicious through this process? 🙂

    Well, thank-you again for all that you do. I really do appreciate your
    recipes. I look good to my family because your recipes taste so good,
    yet my hands did the work. I used your sugar cookie recipe, though I
    used sprouted whole wheat flour. I plan to decorate them with my kids
    today using whatever sweetener we have in the house to make icing.
    I do hope it (the icing) turns out well.

    Thank-you once again.

    Lydia C.

    1. Hi Lydia! Thank you for all the info on sprouted wheat flour! I haven’t tried it in these muffins before, but I’m glad to hear it’s a win in my whole wheat pancakes. Thank you for the extremely kind and thoughtful comment!

  20. so I made these, flavor is great, moisture is not…very dry. I followed perfectly…so is there a way to amp up the moisture

  21. I made these by following your guidance (thanks!) to decrease the egg but sub in more applesauce. So I used 1 egg, halved everything else but used the full amount 1/3 cup of applesauce (I.e. increasing applesauce but halving everything else). I made my own unsweetened applesauce and chopped the apples in tiny bits, otherwise followed tone recipe. I think my adaption worked isn’t terms of flavour and structure as mine tasted hearty but not too oily or dry . I will make this again in the autumn or winter and perhaps will add a handful of dried cranberries (pre-soaked for 10 minutes in warm water) and experiment with the spices – perhaps make my own apple pie spice mix. Thanks Sally for another interesting recipe! Looking forward to seeing your upcoming summer recipes…I might make Zucchini brownies adapting one of your recipes.

  22. Hi sally!
    All I have is whole ground spelt flour. Can I use that as a substitute or nah!?

    1. Hi Sarah! You can definitely try. The muffins will taste on the heavy side.

  23. These sound so good! Could I substitute whole eggs with egg whites?

    1. Hi Patti! I haven’t tried it, but I can’t see why not.

  24. 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.

  25. Really yum! Used the 1/3 vegetable oil instead of applesauce. Didn’t have quite enough maple syrup but they were still delicious.

  26. Hey there! You are truly my favorite address for baking ideas because they ALWAYS turn out great! Now it’s been awhile since I’ve needed some new inspiration and was surprised and disappointed by the changes. 1. I’m so bombarded by ads that I can hardly find your articles. 2. I can’t print out your recipes anymore. Sure copy / paste… but… I’ll still try this recipe, but I’m not sure how many more. Sooo disappointing.

    1. Hi Shay! There was a coding update over the weekend that temporarily disabled the print button. It’s bene fixed this morning. (Sorry, our tech support isn’t available on the weekends!) We also removed 2 ad placements after the update. Sorry for the trouble!

  27. 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!

    1. Thank you so much, Samantha! Thrilled you enjoyed these muffins 🙂

  28. I made these for an as easy breakfast for my 13 month old. He loves them! Thank you!

  29. For some reason my batter was so dry. I tried adding in water but I could never get the batter to be a typical muffin like batter. Just came out like wet sand. I couldn’t grate the apples because it just wasn’t working so I chopped them up really small. What can I do next time? Didn’t seem to be much liquid

    1. Hi Kaelan! Did you make any ingredient substitutions? The only thing I can think of is the apples– shredding the apples makes them extra wet and juicy, which adds a ton of moisture to the batter. You can shred them next time OR add some milk to the batter.

      1. Yes I figured it out! I used coconut flour and apparently it is more absorbent than grain flour so I should’ve only used 1/4 cup per cup of grain flour. I’m trying it again with whole wheat flour and will shred my apples in a food processor and hope that works

      2. These are great! I accidentally left out oil, but had some extra applesauce, you really don’t miss the oil, sugar or anything else, these are delish! I sprinkled some cinnamon sugar on top for looks and extra crunch. Definitely going to make these again.

  30. 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.

    1. I’m so glad to read this! These are some of my favorite muffins and you can never tell that they’re whole wheat. 🙂

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I’m Sally, a cookbook author, photographer, and blogger. My goal is to give you the confidence and knowledge to cook and bake from scratch while providing quality recipes and plenty of pictures. Grab a cookie, take a seat, and have fun exploring! more about Sally