Whole Wheat Apple Cinnamon Muffins

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

Healthy, simple, AMAZING whole wheat apple cinnamon muffins with zero refined sugar. Find this easy muffin recipe on sallysbakingaddiction.com

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! ↓

Healthy, simple, AMAZING whole wheat apple cinnamon muffins with zero refined sugar. Find this easy muffin recipe on sallysbakingaddiction.com

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.

Healthy, simple, AMAZING whole wheat apple cinnamon muffins with zero refined sugar. Find this easy muffin recipe on sallysbakingaddiction.com

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.

Healthy, simple, AMAZING whole wheat apple cinnamon muffins with zero refined sugar. Find this easy muffin recipe on sallysbakingaddiction.com

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.

Healthy, simple, AMAZING whole wheat apple cinnamon muffins with zero refined sugar. Find this easy muffin recipe on sallysbakingaddiction.com

More Favorite Muffin Recipes


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 (226g) 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

Healthy, simple, AMAZING whole wheat apple cinnamon muffins with zero refined sugar. Find this easy muffin recipe on sallysbakingaddiction.com
Healthy, simple, AMAZING whole wheat apple cinnamon muffins with zero refined sugar. Find this easy muffin recipe on sallysbakingaddiction.com


      1. Either the applesauce or part of the oil. I recently made them by substituting 1/3 oil instead of the applesauce, but I was wondering if you could cut out the extra oil and sub applesauce for greek yogurt, or if I would have to use the extra 1/3 of oil when subbing the greek yogurt for applesauce.


  1. These look so yummy. I am a Weight Watcher member and will run this through the recipe builder. But I love the fact that you are not using refined sugar in these. The new WW factors sugar to figure points now. These will make a great snack or quick breakfast with a piece of fruit. Thank you. 
    By the way today I made your lightened up creamy chicken noodle soup so we can have that for dinner tomorrow night. The taste test tells me and my husband that it will be great! 
    Thank you for your wonderful recipes especially the “healthier ones”

  2. Sally these look so yummy! Quick (hopefully not too dim) question: can I leave the skins on the apples, or should they be peeled first? I’m using pink ladies 🙂

  3. Oh my my my.  I made these and they are SO GOOD!  I didn’t quite have 2/3 cup of maple syrup so I finished the 2/3 cup with Agave Nectar.  I used chopped walnuts.  They are highly addictive!  

  4. Hi Sally,
    I have a couple of questions since some ingredients are a little hard to get here in Korea.
    First, can I make the applesauce at home? If yes is there a good recipe?
    And what could I replace allspice with? Is it replaceable?
    Also will using regular flour instead of whole wheat flour change things?
    Thank you always for your delicious treats!

      1. I don’t have allspice either but i do have pumpkin spice, ground cloves,  and ground nutmeg. Would any of these work to substitute the allspice so that there’s less of a loss in flavor?

  5. 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!!!!! 

  6. I love all muffins.  I’m one of those weird people that only like maple syrup on pancakes tho.  Do you think the maple syrup is optional?  A have a recipe for an all veggie chow mein with a bit of added maple syrup and didn’t even notice the syrup.  Do you notice the syrup in this recipe?

    1. Hi Shelly! The muffins won’t be sweet at all without the maple syrup. They might taste like cardboard, at least that’s what I’m imagining! You can try honey instead.

  7. These muffins turned out great, wonderful recipe! I especially liked the combination of walnut, maple syrup and cinnamon – very balanced and it goes really well with apples.
    I had however a not-so-minor problem in the making which was totally my fault: I forgot to preheat the oven! I made these with my 5-year-old and was a little occupied with keeping an eye on him while he grated the apples, and apparently I only turned the switch for the temperature – not the one that actually starts the oven! So I quickly decided to bake them in the gas barbecue with indirect heat, worked surprisingly good. Otherwise the effect of the soda would’ve been nearly gone by the time the oven had the right temperature.
    So: rocksolid recipe, for outdoor-use as well 😉

  8. I made a batch of those muffin and I find something weird.  Are you sure 2 cups of whole wheat flour are 260g? With my flour -and in a equivalence table- 2 cups equivaled to 160g.  I made them with 230g.  They taste good (I used honey and as you said they are not very sweet).  My batter is much more dark (maybe you use whole and all purpose) and solid (or dry). When they were done the top was not smooth and shinning as yours.  If you can, let me know what you think. 

  9. Do you think substituting applesauce with greek yoghurt would work?

    Btw I’ve been reading your blog for like two years, it’s the best food blog ever and it just keeps getting better

  10. i love muffins that aren’t overly sweet!  and using whole wheat flour makes them even better!  thank you so much for this recipe.  i am making it right now.

    if you could do a recipe for maple taffy (the kind on the snow) i would be in heaven!

  11. Hi Sally,
    I started reading your blog a couple months ago and fell in love with your recipes and the clear and detailed way you explain everything. I tell everyone about how I’m learning to bake correctly after years of winging it. I love that this month you have focused on healthier recipes. Have you ever looked into soaking grains? Personally I have never done it, but have done research on it. Basically it makes the whole grains more digestible and nutritious. I would love to have a recipe from you that incorporates this step. I would appreciate it a lot and if a popular blog like yours had a soaked grains recipe a lot more people might try it. Thanks!

  12. I just made these muffins a week ago and they are absolutely delicious!
    However, they did come out fairly dry. Would you have any recommendations for making them moister without sacrificing the taste or the low calorie count?

    1. How about adding 2 Tablespoons of oil? I know the calorie count will be a little higher in each, but it would surely help.

  13. 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 🙂

    1. Gracie, I’ve never baked at high altitude so I have zero experience– but I did have a reader email me recently saying these are fine as is at a higher altitude.

  14. Excellent Muffin!!!
    My husband thought they were phenomenal!!

    My oven is a bit persnickety…following 5 minute burst bake,  the muffins baked in 14 minutes at 350.

    Moist, shiny and delicious!

    Thanks Sally!

  15. I made these this morning. I would love to have some healthy muffins in my repertoire that actually taste good, and I trust Sally’s recipes. I thought these were just OK. They have lots of potential. I love that the sweetness is from maple syrup and applesauce rather than white sugar. If I make them again, I think I will dice the apples rather than grate them and maybe put more in. It just didn’t seem appley enough for us, and I think I would like to bite into small pieces of apples. (In the recipe’s defense, I didn’t measure my grated apple. I had two rather large apples and just assumed that grating them would result in enough apple, but now I’m wondering if it wasn’t quite two cups.) The muffin was slightly drier than I would prefer — not sure if more apple would take care of that. If not, I would add a bit more oil. Definitely on the right track but as it turned out this morning it is not a muffin I would get excited to eat.

  16. 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!

  17. Amazing! These are so delicious and the perfect amount of sweet without sugar!!!!! Keeper recipe for apple season!! Thank you as always! 

  18. 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.

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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