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. How many calories is in this recipe? Thanks 🙂

    1. Hi Bee, I’m unsure of the nutritional information of this recipe, but there are many great online calculators like this one: https://recipes.sparkpeople.com/recipe-calculator.asp

  2. Made these yesterday, and they were pretty good! I made a few substitutions based on the ingredients I had; I replaced 1/3 cup of the maple syrup with 1/3 cup coconut sugar, used all-purpose flour instead of whole wheat (simply because I didn’t have it in my pantry, though I hope to use it next time), and replaced the applesauce with an equal amount of melted butter. As I said, they were pretty delicious, but there are a few changes I want to make next time: (1), the apple flavor wasn’t as pronounced as I would like, probably because I omitted the applesauce, so I plan to add apple chunks in along with the grated apple. (2), a little less cinnamon; I found that 2 teaspoons overpowered the apple, and while I love cinnamon, I still want to taste the apple, so next time I’ll reduce it to 1 1/2 teaspoons. Aside from that, they looked and tasted great, and they smelled AMAZING while baking; I had them in the oven while preparing stew for dinner, and got to inhale the tantalizing aroma the entire time 🙂 Someone ought to take the scents of baked goods as they’re baking and bottle it; I’d wear a perfume like that any day!

  3. Cant wait for my kids to have these for breakfast. They look and smell delicious

  4. Hi Sally, I baked these muffins with raisins instead of apples yesterday. They turned out a little too dry.
    Is it because I used raisins instead of apples?
    Or because I over- folded the mixture?

    What will make a good substitution for the apples? Cherries? Oranges? Raspberries?

    If I were to use apples, how do I keep the apples from turning brown once I cut them?
    Can I cut them into chunks instead of grating them?

    Given the initial baking temperature of 217 degrees, Is it alright to use rapeseed oil for this recipe?

    1. Hi Sarah, Yes the apples act as a wet ingredient so if you skip them the muffins will be too dry. For other flavors feel free to brose all of my muffin recipes OR use my master muffin mix to create your own!

  5. Sally, these are delicious! The only thing I did differently was to exchange the whole wheat flour with half white whole wheat and half AP.
    I have tried several of your recipes, and found most delicious! Thank you for sharing!

  6. I just made these and there amazing! I only used 1 apple and replaced the oil with olive oil and the apple sauce with yogurt. Definitely recommend these especially for a cold day since these feel so cozy 🙂

  7. If I want to make jumbo muffins, how long should it take to bake these?

    1. Hilari @ Sally's Baking Addiction says:

      Hi Lynn, 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!

  8. I made these 2 days ago and they were great. I only had wholemeal flour but I decided to go totally rogue and hand grind some whole wheat course grain bulgur (about 3/4 cup) and 1/2 cup LSA meal mix instead of the full 2 cups flour. I added crushed walnuts as well as I didn’t have quite enough pecans. I also randomly added 2 table spoons of puffed amaranth. I didn’t have the applesauce so I used the 2/3 cup coconut oil as recommended. Otherwise I followed the recipe exactly. These muffins are so good. They have an incredibly healthy taste and that whole grain savouriness I was craving! My chef partner admired them although wanted them sweeter, but for me they are perfect. My only change next time would be to make an apple sauce because the coconut oil flavour was a little dominant over the apple. Ps the tip about starting at high temp worked really well.

  9. I tried this recipe today, halving all ingredients. I replaced the applesauce with Greek yogurt and added chocolate and peanut butter chips. The result came out beautifully! The muffin is still moist and soft, and delicious! Thank you for this recipe Sally.

  10. Sally God bless you! These were the best cinnamon apple muffins I’ve ever tried! I didn’t have pecans so I omitted that, and used coconut oil…so delicious. Thank you for sharing this wonderful recipe!

  11. My favorite go to muffin recipe!

  12. This is one of the best muffin recipes I’ve tried with all whole-grain flour (and I’ve tried a lot of them). Very light in texture, full of flavor, and thoroughly satisfying!

  13. Great muffins. I made them exactly as directed and they came out perfect. The allspice is the magic ingredient! Everyone commented on how good they smelled before they even took a bite.
    Thank you for the recipe!

  14. Looking forward to trying these! What can I replace the applesauce with? Can I use plain greek yogurt and how much? Thank you

    1. Lexi @ Sally's Baking Addiction says:

      Hi Kim, Greek yogurt (same amount) would work, or you can use an additional 1/3 of oil. Hope you enjoy them!

  15. I followed the recipe exactly and these are soo delicious! Almost too delicious! How can stop after just one lol! Can’t wait to browse some of your other recipes 🙂

  16. These muffins are great. Just made them the second time, first time they were perfect and moist, second time they were drier. Second time I couldn’t grate the apple though (had to chop) and used coconut oil instead of canola, plus I’m using an oven that seems to cook hotter. On this second time though I made maple glaze from your maple scone recipe. Used Grade B syrup and subbed maple sugar for 1/4 of the powdered sugar then dunked these puppies in. It’s absolutely dreamy. The remaining maple glaze is going to get drizzled over the Guinness frosting on your Guinness brownies in two weeks!

  17. Can I substitute the Allspice with something? I don’t know if I can get a hold of it.

    1. Trina @ Sally's Baking Addiction says:

      Hi Maxim! You can leave out the allspice.

  18. OMG, I just made these and they came out so amazing! The only modifications I made was using only 1/3 cup maple syrup and using olive oil. I’m so impressed with how great they came out. Thank you!

  19. Emma Burrows says:

    are these okay for a lactose free person

  20. Thank you for the delicious recipe, Sally! I made this recipe today and the muffins turned out amazing. The only add on was 1/4 cup of brown sugar, since I did not have enough maple syrup.

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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