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

whole wheat apple cinnamon muffins

overhead image of whole wheat 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 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

More Favorite Muffin Recipes

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3 images of whole wheat apple cinnamon muffins

Healthy Whole Wheat Apple Muffins

  • Author: Sally
  • Prep Time: 15 minutes
  • Cook Time: 24 minutes
  • Total Time: 40 minutes
  • Yield: 12 muffins 1x
  • Category: Muffins
  • Method: Baking
  • Cuisine: American


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


  • 2 cups (250g) whole wheat flour* (spoon & leveled)
  • 1 teaspoon baking soda
  • 1 teaspoon baking powder
  • 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*
  • 2/3 cup (160ml) pure maple syrup
  • 1/3 cup (80ml) melted coconut oil (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: 1/2 cup (65g) chopped pecans or walnuts


  1. Preheat oven to 425°F (218°C)6. Spray a 12-count muffin pan with nonstick spray or use cupcake liners.
  2. In a large bowl, whisk the flour, baking soda, baking powder, 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 grated apple and pecans/walnuts. Fold everything together gently just until combined and no flour pockets remain. The batter is very thick.
  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 17-18 minutes or until a toothpick inserted in the center comes out clean. The total time these muffins take in the oven is about 22-23 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. Whole Wheat Flour: 2 cups of white whole wheat, whole wheat pastry flour, or all-purpose flour work too. We have not tested this recipe with gluten free flours, but here are some gluten free blueberry muffins.
  3. Maple Syrup: For best results, use pure maybe syrup, not breakfast syrup. You can substitute honey if needed, but reduce the honey to 1/2 cup (170g).
  4. 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.
  5. 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.
  6. Nutrition Information: Using SparkRecipes calculator, these muffins come out to 184 calories, 8g fat, 25g carbs each.

Keywords: apple cinnamon muffins, whole wheat apple muffins

Reader Questions and Reviews

  1. 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.

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

    1. 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.

  3. 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!

  4. 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!

  5. These are delicious, Sally!

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

    1. 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!

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

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

  8. 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. 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?

    1. 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!

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

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

  11. Hi Sally…I’m wondering if I can omit the oil and just increase the applesauce?

    1. Hi Linda, Without any fat, the muffins will have a rubbery texture. We don’t recommend replacing the oil altogether.

  12. Made two batches of these. Recipe was easy to follow. Didn’t add any nuts as I didn’t have any. Very happy with the recipe, thank you!!

  13. These were delicious! Thank you for sharing this recipe! Next time I would like to use the Jumbo muffins tins- do you recommend I keep the temps the same, just that I cook it longer at 350?

    1. Hi Kristin! For jumbo muffins, 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!

  14. What a great recipe! I’m a guy who has never baked but love baked goods. Too much, lol! So I made these with whole wheat flour, no sugar or syrup or honey, just sweetness from applesauce, raisins, apples, and I add a grated carrot. Spectacular! have been making them almost weekly. Today switched up and made banana walnut. Next week orange cranberry. I feel so empowered, lol! It’s so flexible and forgiving. I also hate those sprays so I followed a neighbor’s advice and just wet the muffin pan with water. Brilliant! They slipped right out and clean-up was a snap. She said she learned this trick from a french chef. Thank you so much for helping me find a great healthy snack.

    1. Hi Jeff – your changes sound great for my dietary needs. What did you sub for the maple syrup to make up for the lost wetness of the batter? And thanks, Sally, for a luscious, healthy muffin recipe?

  15. These muffins are absolutely delicious! Thanks so much for sharing, these will be a weekly treat in my house!

  16. I made these muffins with my 3 year old granddaughter and they were a big hit! I omitted the nuts for an equal amount of raisins. I was skeptical about using whole wheat flour but they were moist and tender. They kept wonderfully in an airtight container for several days and reheated them on subsequent mornings in the microwave for about 30 seconds. These healthy, scrumptious muffins have become a staple in my breakfast recipes! Great for an afternoon snack, too.

    1. Hi Katie, the flavor will be different, but olive oil will work!

  17. These are FANTASTIC! Super easy and SO flavourful! Sally has done it again! 🙂

  18. Firstly – this recipe was absolutely delicious, so happy I tried it! The muffins were a huge hit with my family, including with my partner – who is not even an apple fan!

    What would your recommendation be if I wanted to replace all of the maple syrup with brown sugar? I’m wondering if I can add some greek yogurt to add moisture back in, and if I can, how much you’d recommend.


    1. Hi Vicky, so glad you loved these muffins! That swap would require some testing, but it sounds like you’re on the right track. Let us know what you try!

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