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. 

Apple muffins topped with cinnamon sugar on a cooling rack.

Healthy Apple Cinnamon Muffins

Brittany Mullins
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.
5 from 5 votes
Prep Time 15 mins
Cook Time 35 mins
Course Breakfast
Cuisine American
Servings 12
Calories 185 kcal

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 1-2 apples

Topping

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

Instructions
 

  • Preheat oven to 350°F. Line a muffin pan with cupcake liners or coat with cooking spray.
  • 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.
  • In a small bowl, mix together the topping - 2 Tablespoons of sugar with 1 teaspoon cinnamon.
  • In a medium bowl, whisk together the all-purpose and whole wheat flour, baking soda, baking powder, cinnamon and salt.
  • 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.
  • Fold the flour mixture into the wet mixture. Gently stir in the apple chunks.
  • 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.
  • Let cool on a wire rack for 15 minutes. Store any leftover muffins in the refrigerator for up to 3-4 days.

Video

Notes

  • For vegan muffins: use Earth Balance Buttery Stick instead of butter and coconut milk yogurt instead of regular Greek yogurt.

Nutrition

Serving: 1muffinCalories: 185kcalCarbohydrates: 31gProtein: 5gFat: 5gFiber: 4gSugar: 13g
Keyword healthy apple muffins
Tried this recipe?Let us know how it was!
This post may include affiliate links. Thank you for your support.

Leave a Comment

Your email address will not be published. Required fields are marked *

Recipe Rating




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

      5 stars
      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

      5 stars
      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

      5 stars
      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

      5 stars
      Yum!! Super simple to make

Parchment paper lined with protein balls.

5 SECRETS TO
HEALTHY SNACKING

Eating healthy doesn’t have to be boring!

FREE EMAIL BONUS