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 (affiliate link) 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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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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    43 comments
  1. 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.

    • 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

  2. 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… 🙂

  3. 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.

    • 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.

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

    • 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.

  5. 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.

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

  7. 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!! 🙂

  8. 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!

  9. LOVE that these don’t have eggs in them 😀 I’m so not a fan of eggs lol apples and cinnamon are prob the best combo in my book, I’ll totally try these out 🙂

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