Healthy Apple Cinnamon Muffins

These healthy apple cinnamon muffins are made with a blend of whole wheat and all-purpose flour. They’re loaded with fall flavor and extra moist thanks to pumpkin! Vegan modifications included.

Almost every fall we go apple picking at a local orchard and bring home a ton of apples! I love eating apples on their own or with nut butter so we can easily make it through what we pick, but typically I also get the urge to make a delicious baked good with the fresh apples too. Apple muffins popped into my head so that’s what I’m sharing today!

Isaac tasted one and said they were his favorite baked good I’d made in a while! With a comment like that, I pretty much had to make another batch for him this week. I’m not mad about it…

Apple muffins topped with cinnamon sugar on a cooling rack.

These muffins are hearty, moist, and have the perfect amount of sweetness from the brown sugar and apple chunks. As with most muffins, they’re great paired with a cup of coffee on a chilly fall morning.

Ingredients in Healthy Apple Muffins

This apple muffin recipe is much healthier than your average muffin, with all-natural ingredients whole wheat flour, plain Greek yogurt, fresh apples, and flaxseed. I also used canned pumpkin in the recipe so I could cut back the amount of butter. You could certainly use 3/4 cup applesauce or go the decadent route and use the extra 1/4 cup of regular (or vegan) butter instead of the pumpkin. You all know I love my pumpkin so obviously, it makes sense that I like the pumpkin version best — even if it’s not the star of the show in this recipe.

A healthy apple muffin cut in half. Muffin is full of apple chunks.

How to Make Healthy Apple Muffins

Line a muffin pan with paper liners or silicone liners for easy cleanup or coat with cooking spray. In a small bowl, whisk the ground with water to make the flaxseed egg. Let sit while you prep the rest of the ingredients. In another small bowl, mix together the topping and set aside.

Whisk the dry ingredients together in a medium bowl. In a medium bowl, whisk together the quinoa and whole wheat flour, baking soda, baking powder, cinnamon, and salt. In a large bowl, mix the sugar with softened butter until combined. Add the flaxseed egg, pumpkin, and vanilla. Stir in the Greek yogurt. Fold the dry ingredients into the wet mixture. Gently stir in the chopped apple. Divide the batter into the prepared muffin pan and sprinkle with the brown sugar topping. Bake in a preheated oven for 25-30 minutes or until a toothpick inserted in the center of the muffin comes out clean. Let the muffins cool on a wire rack for 15 minutes and store any leftovers in an airtight container in the refrigerator for 3-4 days.

Apple muffins topped with cinnamon sugar on a cooling rack.

Believe me when I say that the tops are the best part — so sweet and cinnamony. Hopefully, you love them as much as we do!

Healthy apple muffins in a muffin tin.

Want More Delicious Muffin Recipes?

If you make these healthy apple cinnamon muffins, please be sure to leave a comment and star rating below. Your feedback is super helpful for the EBF team and other readers who are thinking about making the recipe. 

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Apple muffins topped with cinnamon sugar on a cooling rack.

Healthy Apple Cinnamon Muffins


  • Author: Brittany Mullins
  • Prep Time: 15 minutes
  • Cook Time: 35 minutes
  • Total Time: 50 minutes
  • Yield: 12

Description

These healthy apple cinnamon muffins are made with a blend of whole wheat and all-purpose flour. They’re loaded with fall flavor and extra moist thanks to pumpkin! Vegan modifications included.


Ingredients

  • 1/4 cup (4 Tablespoons) butter, softened*
  • 3/4 cup coconut sugar or brown sugar
  • 3/4 cup plain non-fat Greek yogurt*
  • 3/4 cup canned pumpkin
  • 2 Tablespoons ground flaxseed + 6 Tablespoons water (or 2 regular eggs)
  • 1 teaspoon vanilla
  • 1 cup all-purpose flour
  • 1 cup whole wheat flour
  • 1 teaspoon baking powder
  • 1 teaspoon baking soda
  • 1/2 teaspoon cinnamon
  • 1/4 teaspoon sea salt
  • 1 1/2 cups peeled and finely chopped apple pieces (about 12 apples)

Topping

  • 2 Tablespoons coconut sugar or dark brown sugar
  • 1 teaspoon cinnamon

Instructions

  1. Preheat oven to 350°F. Line a muffin pan with cupcake liners or coat with cooking spray.
  2. In a small bowl, whisk together the 2 Tablespoons of ground flaxseed with the 6 Tablespoons of water and let sit while you start preparing the other ingredients.
  3. In a small bowl, mix together the topping – 2 Tablespoons of sugar with 1 teaspoon cinnamon.
  4. In a medium bowl, whisk together the all-purpose and whole wheat flour, baking soda, baking powder, cinnamon and salt.
  5. In a large bowl, mix the 3/4 cup sugar with the softened butter until combined. Add the flaxseed/water mixture, pumpkin and vanilla. Stir in yogurt.
  6. Fold the flour mixture into the wet mixture. Gently stir in the apple chunks.
  7. Pour the batter into the prepared muffin pan and sprinkle with the brown sugar topping. Bake for 25 to 30 minutes or until a wooden pick inserted in center of 1 of the muffins comes out clean.
  8. Let cool on a wire rack for 15 minutes. Store any leftover muffins in the refrigerator for up to 3-4 days.

Notes

  • For vegan muffins: use Earth Balance Buttery Stick instead of butter and coconut milk yogurt instead of regular Greek yogurt.
  • Category: Breakfast
  • Method: Bake
  • Cuisine: American

Nutrition

  • Serving Size: 1 muffin
  • Calories: 185
  • Sugar: 13g
  • Fat: 5g
  • Carbohydrates: 31g
  • Fiber: 4g
  • Protein: 5g

Keywords: healthy apple muffins

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    52 comments
    1. Jackie
      November 11, 2020 AT 1:01 pm

      They are so delicious! Super moist, tons of flavor. I subbed the flours with gluten free options (1 cup almond flour, 1 cup 1-1 flour) and they are incredible.

      1. Brittany Mullins
        November 11, 2020 AT 8:14 pm

        yay!! So glad these muffins turned out for you with the almond + gluten-free flour, Jackie. Thanks so much for coming back to share that, it’s super helpful for future readers. 🙂

    2. Brogan
      September 28, 2020 AT 9:44 am

      Just made these this morning and they turned out AMAZING! I used 2 cups of white whole wheat flour instead of 1c APF and 1c whole wheat flour. My friend also subbed and did 1c oats and 1c flour and it worked out perfectly for her! Also I skipped the topping but I’m sure it would have been delicious. Thank you, Brittany!

      1. Brittany Mullins
        September 28, 2020 AT 2:42 pm

        Oh yay!! So glad these muffins turned out for both you and your friend. Thanks for sharing what subs you guys made. It’s super helpful for other readers, so I appreciate it. <3

    3. Clare
      September 20, 2020 AT 9:33 am

      Made these on a fresh fall morning and the family woke up to a delicious smell! I am so glad I stumbled across this recipe, they won’t stop going on about how absolutely delicious these muffins are! (Even a yogurt-hater just adores them!)

      1. Brittany Mullins
        September 23, 2020 AT 1:58 am

        Woo!! That makes me so happy to hear. 🙂 I’m so glad these muffins were a hit with your fam. Thanks so much for making these and for coming back to leave a comment + star rating. I really appreciate it.

    4. Sarah Blanchette
      September 6, 2020 AT 11:26 pm

      These muffins are the best!! I was wondering if its ok to put them in the freezer?

      Thank you!

      1. Brittany Mullins
        September 7, 2020 AT 5:39 pm

        Totally! They should store just fine in an airtight container in the freezer. 🙂

    5. Katie
      April 26, 2020 AT 12:52 pm

      Yum!! Super simple to make

    6. stacy
      October 22, 2019 AT 1:01 am

      always looking for baked goods with whole wheat flour. this recipe came out great and my picky kids can’t get enough. i used the eggs and whole milk greek yogurt, so that didn’t hurt and even used an extra 1/4 cup whole wheat instead of regular. also a huge fan of coconut sugar and pumpkin is always YUMMY. I’m going to try the pumpkin bars next. oh – and love that i didn’t have to use liners. greased tins with coconut oil.

      1. Brittany Mullins
        October 22, 2019 AT 1:13 pm

        Woo-hoo! So glad you and your kids enjoyed this recipe, Stacy! Thanks for trying it and for coming back to leave a comment and star rating. The ratings are super helpful so I really appreciate it! <3

    7. Charlane
      October 3, 2019 AT 7:21 pm

      Brittany, your timing was perfect with the Apple Cinnamon muffin recipe! I am working through A LOT of apples right now and the pumpkin was a great addition! (I confess I also added toasted walnuts – because I’m nuts about nuts!). Even without they are moist and, well, perfect! A huge hit in my house! Making more for the freezer… 🙂

      1. Brittany Mullins
        October 4, 2019 AT 9:16 am

        Yay!! I am so glad that the muffins were such a hit. Thanks so much for sharing, Charlane.

    8. Melissa
      October 1, 2019 AT 6:49 pm

      I’m just about to make these and I saw there were asterisks after the butter and Greek yogurt. Is there something about them I’m missing. I’m making this with pumpkin so I want to make sure I’m supposed to add butter when using the pumpkin. Thanks! Can’t wait to make them.

      1. Brittany Mullins
        October 1, 2019 AT 10:34 pm

        The asterisks just mean that there are notes down below about the ingredients. The notes are about how to make the recipe dairy-free. Hope this helps. Let me know how the muffins turn out for you.

    9. Nancy
      September 26, 2019 AT 1:24 pm

      Hi Brittany! 🙂
      Do you think I can use Almond flour or Coconut flour instead of the all purpose & whole wheat flours?
      They look delish!

      1. Brittany Mullins
        September 26, 2019 AT 2:57 pm

        Hi Nancy! I think you could easily use an all-purpose gluten-free 1:1 flour for the full amount of flour. I can’t speak to coconut or almond because I haven’t tested it. Let me know if you try it and how it turns out for you.

    10. Jeni
      September 25, 2019 AT 10:38 am

      Have you made these with gluten free flours? I would love to try them but would need to make them GF. Do you think I can sub 1:1? I have not substituted with recipes that call for white and whole wheat flours together.

      1. Brittany Mullins
        September 25, 2019 AT 4:39 pm

        Hi Jeni. I haven’t tried it, but I think you could easily use an all-purpose gluten-free 1:1 flour for the full amount of flour. Let me know if you try it.

    11. Mary Anne
      September 8, 2019 AT 7:50 pm

      How do I remove the black box that advertises a new recipe “get recipe”. The is no “close” option and it blocks the recipe

      1. Brittany Mullins
        September 9, 2019 AT 10:10 pm

        Ugh! I’m so sorry you’re dealing with this. I’ve contacted my ad network and had it removed.

    12. Dottie
      July 5, 2019 AT 11:37 pm

      I don’t have Flaxseed, is there anything else I can use? Thanks 🥰

      1. Brittany Mullins
        July 8, 2019 AT 8:18 am

        Hi Dottie. The flaxseed + water combo is a replacement for eggs. If you don’t have flaxseed, just use 2 eggs instead of the flaxseed and water. 🙂

    13. Tara Rodman
      September 23, 2014 AT 2:19 pm

      Anyone wanna take a stab at how many calories might be in these muffins? Roughly?

      1. Brittany Mullins
        September 25, 2014 AT 11:29 pm

        Hi Tara. Just added the nutritional stats to this recipe! They have about 185 cals per muffin.

    14. suz
      October 1, 2013 AT 3:25 am

      Could I leave the pumpkin out? Or use something else instead? Maybe butternut squash?

    15. Sagami
      September 11, 2013 AT 11:01 am

      Can I use Oat flour instead of wheat?

      1. Brittany Mullins
        September 11, 2013 AT 10:57 pm

        I think that would work fine.

    16. Kristie
      December 1, 2012 AT 8:10 pm

      So glad you shared this recipe. I’ve been looking for new ways to add a little extra fiber to my diet and these are so delicious. I was cutting them in half and reheating with a little bit of olivio on them but they don’t even need that…they are great on their own. Love them! Thanks!! 🙂

      1. Brittany Mullins
        December 1, 2012 AT 11:56 pm

        So glad you like them Kristie!

    17. Katie @ Oh Shine On
      October 31, 2012 AT 11:58 am

      I need to bake me some of these!

    18. Lauren @ The Homeostatic Mindset
      October 30, 2012 AT 4:40 pm

      This is PERFECT!!!!! I have been scouring Pinterest for a yummy Apple Cinnamon muffin, and here it is! Will be making these sometime soon! Maybe tomorrow?! To celebrate Halloween + being done a midterm! 🙂

    19. School of medicine
      October 25, 2012 AT 3:39 am

      The the information you are providing is really helpful to me .keep posting.

    20. Grace @ Practicing Grace
      October 24, 2012 AT 2:30 pm

      I went to UVa so I feel very fondly for that entire area. The hiking, apples, mountains. Sigh. And I also can’t wait to try this recipe!

      1. Brittany Mullins
        October 24, 2012 AT 9:19 pm

        So cool! I grew up in Orange, VA so I’m pretty fond of that area too. 🙂

    21. Lisa
      October 24, 2012 AT 10:12 am

      We went out to Carter Mountain last weekend and grabbed some of our own. So far I’ve done an apple pie baked oatmeal for breakfast, and HomeMan made a dessert pizza like the ones on pizza buffets with his homemade crust! Whatever we have left will go into crock pot applesauce on Saturday, but I might have to try this recipe out first!

      1. Brittany Mullins
        October 24, 2012 AT 9:21 pm

        Oh yum – everything you all made sounds awesome. I think I need some apple pie baked oatmeal in my life!

    22. Jess @ JessieBear What Will You Wear
      October 23, 2012 AT 10:00 pm

      these. look. delicious.

    23. purelymichelle
      October 23, 2012 AT 9:18 pm

      can you send some my way 😉

      1. Brittany Mullins
        October 24, 2012 AT 9:24 pm

        I would, but they are gone already. 😉

    24. Lauren
      October 23, 2012 AT 5:27 pm

      These look so good Brittany! Way better than mine. 🙂 I need to take baking tips from you girl.

    25. janetha {meals & moves}
      October 23, 2012 AT 4:13 pm

      These look great, lady!

      1. Brittany Mullins
        October 24, 2012 AT 8:37 am

        Thank you dear! We need to catch up soon – I feel like we haven’t seen each other/emailed in ages.

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