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. Would these work with peaches, canned or frozen? I’ve made them as is several times, love the recipe. Would like to keep the base and switch things up.

    1. Lexi @ Sally's Baking Addiction says:

      Hi Christine, that should work fine, just be sure to drain and blot any extra moisture from the peaches as they’ll add more liquid to the batter than the apples. Or, you might like our Peach Streusel Muffins as well!

  2. Absolutely delicious!! The BEST apple cinnamon muffins recipe ever!!! I love the fact that they are healthy and sooo fresh and moist and yummy. Thank you so much!!

  3. Will it be okay to use all white whole wheat four? Thank you!

    1. Hi Michele, you can use white whole wheat flour instead. Same amount.

  4. Made these today with grapeseed oil (instead of coconut), honey (instead of maple), homemade applesauce instead of grated apple (quicker) and added 3/4 cup/75g whole oats otherwise I followed the recipe exactly. My add ins were hemp seeds, chopped and toasted walnuts and an apple chopped (to use up old apples). Light, fluffy and moist wholemeal muffins, so so good! The hot air trick is genius, thank you for the recipe.

  5. Good evening! I would love to make these a head of time, for a gathering. Could I freeze these? They look awesome

    1. Lexi @ Sally's Baking Addiction says:

      Hi Sarah, absolutely! 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.

  6. Hey Sally! FIrst things first (I promise I have a question but I have to say this first) OMG thank you for helping me discover my sincere LOVE of baking. Like I literally just sold all my stuff so I can go to baking school thanks to this blog. Your recipes put to paper the ideas I have, and I’ve been able to learn better food science because of your detailed posts. This has been a huge win for me during an uncertain time, after 10 years of trying to find my passion. So… YOU GO GIRL!!!!

    I’ve been playing with your master muffin recipe and am excited to try this healthier one now (due to the many jumbo full fat muffins I’ve consumed in the last 4 months).

    Just wondering if I could substitute in some oats… say 1/3 of the flour swapped? I was also curious, most of your other muffin recipes call for sour cream or yogurt. Is the reason it was omitted from this recipe because the maple syrup is more moist than the granulated sugar? I am considering doing the recipe above but doing half maple syrup, half brown sugar, so curious if I should add maybe… 1/4 cup of yogurt?


    1. Hi Abbey! I’m just seeing this wonderful comment and question now! Thank you for your incredible kindness. It’s so nice to hear from you and I’m so happy to read that my recipes have inspired you in such a profound way! Best of luck to you on this new chapter. 🙂

      Regarding this muffin recipe, you could certainly add some oats. I think if you’re making the other changes (half maple syrup, half brown sugar) that you could replace 1/3 cup of flour with 1/3 cup of oats. Add some yogurt or sour cream since you’re reducing the maple syrup. Even 1/4 cup could help. I’m interested to hear how they turn out!

  7. I made these muffins last week and they are really delicious!
    As much as I love the butter-and-sugar world of baking, I try to mix it up with healthier options sometimes.
    What I love about these and the whole wheat banana nut muffins (thank you for that recipe too) is that, while it’s a lighter version of the traditional muffin, the flavour hasn’t been sacrificed.
    Thanks a bunch for these awesome recipes!

  8. These are delicious, Sally!

    Any advice for reheating a batch for a brunch? I made them a day ahead. Thanks!

    1. Trina @ Sally's Baking Addiction says:

      Hi Kennedy! You can cover the muffins in foil and bake at 350 for 5-10 minutes, then check to see if they’re warm. The trick is warming them without drying them out – let us know what you try!

  9. Sally, your recipes stand the test of time, looking back when this recipe was first published and you are still getting comments! Thank you for your work to bring your readers such well-tested recipes.

    I made these tonight because I wanted something a little more healthy for my visiting 10 year old grandson. My only substitution was using 1 cup applesauce as I did not have any apples. I threw in 1/4c homemade yogurt that wouldn’t fit in the jar. Mine did not bake as high or pretty as yours but I didn’t expect it with no shredded apples. They tasted delicious, and I did not taste the maple syrup as overpowering at all. Used Penzy’s Pie Spice, which gives them a more complex spice flavor I think. Nice to have a little warm spice in August:)

    1. Trina @ Sally's Baking Addiction says:

      We’re thrilled you enjoyed these muffins, Cindy! Thank you so much for making and trusting our recipes 🙂

  10. Pria Paruman says:

    Absolutely delicious!! So simple too. Thanks Sally. Shared this recipe with those I know!

  11. First off thank you Sally for your delicious recipes! I started baking during Covid and I am a huge fan of your website! I have made this apple muffins recipe using small chopped apples from our golf course and homemade apple sauce from the same apples.
    I would like to make another batch as I still have leftover apples and to thank the staff at the golf course. My question is I want to make them without the nuts because of nut allergy and make them a little bit sweeter because the apples are tart. Should I increase the amount of apples and the amount of honey? How much? and can I put chocolate chips?

    1. Lexi @ Sally's Baking Addiction says:

      Hi Tanya, thank you so much for the kind note and feedback! You can certainly omit the pecans OR swap them for chocolate chips as you mention. We don’t recommend increasing the amount of honey as that will add more liquid to the batter and they may not bake up correctly — likewise with the apples. How about adding some coarse sugar on top before baking for a sweet and crunchy kick?

  12. Mary Anne Kennedy says:

    Can I add oatmeal to this recipe?

    1. Stephanie @ Sally's Baking Addiction says:

      Hi! You could certainly try adding some oats. We haven’t tested it but we would start by replacing 1/3 cup of flour with 1/3 cup of oats. Let us know if you give it a try!

  13. Muffins came out So good. Flavour and smell was awesome. Definitely will make again. Thanks Sally for sharing really good recipe..

  14. This has been my standby whole wheat muffin recipe. I use 1.5 cups of white whole wheat flour and a half cup of oat flour made by processing rolled oats in my mini food processor. They always come very moist and delicious. Id like to try adding a little streusel topping before baking. Will that work?

    1. Trina @ Sally's Baking Addiction says:


  15. Thank you for your recipes. Do you peel the apples?
    Thank you,

    1. Lexi @ Sally's Baking Addiction says:

      Hi Judy, you can do either — it won’t make a difference in the recipe either way. Enjoy!

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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