Healthy Apple Cinnamon Muffins

VG

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!

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 easily make it through what we pick, but I typically get the urge to make a delicious baked good with fresh apple too. Apple muffins popped into my head so that’s what I’m sharing today!

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.

Apple muffins topped with cinnamon sugar on a cooling rack.

What Types of Apples Are Best to Bake With?

Typically, I like to use a mix of apples that are sweet but tart and firm so that it holds up well to baking – if apples get mushy while baking, it’s a no-go for me! Honeycrisp, Pink Lady, and Granny Smith are fantastic apples to bake with.

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

Ingredients in Healthy Apple Cinnamon Muffins

  • flaxseed – used with water to make a flaxseed egg as a binding agent. Flaxseed is also rich in nutrients and protein!
  • whole wheat flour – packed with protein, fiber, vitamins and minerals, it is really easy to bake with and provides and added boost of nutrients! I use Bob’s Red Mill 100% Stone Ground Whole Wheat Flour.
  • baking powder and baking soda – leavening agents.
  • cinnamon – cinnamon with apple is the ultimate fall flavor combo. You’ll also use some for the topping.
  • sea salt – brings all the flavors together.
  • coconut sugar – the less-processed upgrade for brown sugar. You’ll also use some for the topping.
  • butter – a tried and true ingredient for giving muffins that moist and delicious texture.
  • pumpkin – adding some pumpkin to this recipe helps cut back on the amount of butter and amps up the fall flavors! Make sure you use pumpkin puree not pumpkin pie filling! You can also make your own pumpkin puree. You could certainly go the decadent route and use all butter instead of pumpkin.
  • vanilla – the perfect flavor enhancer!
  • Greek yogurt – plain non-fat Greek yogurt keeps these muffins moist, no dry muffins here!
  • apple – you’ll need about 1-2 apples, peeled and finely chopped into pieces.
tip!
To make these muffins vegan, use Earth Balance Buttery Stick instead of butter and non-dairy yogurt instead of regular Greek yogurt!

Easy Substitutions

  • flaxseed – if you’re not worried about making these vegan or egg-free, you can definitely use 2 eggs instead!
  • whole wheat flour – if you don’t have whole wheat flour on hand, you can use all-purpose flour! To make this recipe gluten-free you could sub in an all-purpose gluten-free 1:1 flour. I like the Bob’s Red Mill Gluten-Free 1:1 Baking Flour.
  • pumpkin – don’t have pumpkin on hand or want to amp up the apple flavor? You can substitute with homemade applesauce, instead!
  • coconut sugar – you can use brown sugar if you prefer or have it on hand.
Apple muffins topped with cinnamon sugar on a cooling rack.

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 enjoy!

Storing Leftover Muffins

It’s crucial to let these muffins cool completely before storing them. Always let your baked goods cool completely on a wire rack before putting them into a storage container! If you skip this step, the heat creates condensation/moisture and you’ll end up with soggy muffins. Not exactly what we want!

I recommend storing them in the fridge rather than on your countertop. They’ll last longer and they taste delicious straight from the fridge. These muffins will last up to 3-4 days in the fridge or up to 3 months in the freezer. 

Healthy apple muffins in a muffin tin.

Want More Delicious Muffin Recipes?

More Apple Recipes

Healthy Apple Cinnamon Muffins

4 from 12 votes
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!
Apple muffins topped with cinnamon sugar on a cooling rack.
Prep Time 15 minutes
Cook Time 30 minutes
Total Time 45 minutes
Servings 12

Ingredients

  • 2 Tablespoons ground flaxseed + 6 Tablespoons water, or 2 regular eggs
  • 2 cups whole wheat flour
  • 1 teaspoon baking powder
  • 1 teaspoon baking soda
  • ½ teaspoon cinnamon
  • ¼ teaspoon sea salt
  • ¾ cup coconut sugar, or brown sugar
  • 4 Tablespoons butter, softened
  • ¾ cup canned pumpkin or homemade pumpkin puree
  • 1 teaspoon vanilla
  • ¾ cup plain non-fat Greek yogurt
  • 1 ½ 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 ¾ 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 or up to 3 months in the freezer.

Video

Notes

  • for vegan muffins – use Earth Balance Buttery Stick instead of butter and non-dairy yogurt instead of regular Greek yogurt.
  • flaxseed – if you’re not worried about making these vegan or egg-free, you can definitely use 2 eggs instead!
  • whole wheat flour – if you don’t have whole wheat flour on hand, you can use all-purpose flour! To make this recipe gluten-free you could sub in an all-purpose gluten-free 1:1 flour. I like the Bob’s Red Mill Gluten-Free 1:1 Baking Flour.
  • puréed pumpkin – don’t have pumpkin on hand or want to amp up the apple flavor? You can substitute with homemade applesauce, instead!
  • coconut sugar – you can use brown sugar if you prefer or have it on hand.

Nutrition

Serving: 1muffin Calories: 191kcal Carbohydrates: 34g Protein: 4g Fat: 5g Saturated Fat: 2g Monounsaturated Fat: 1g Cholesterol: 11mg Sodium: 181mg Potassium: 223mg Fiber: 3g Sugar: 18g
Course: Breakfast
Cuisine: American
Keyword: healthy apple muffins

DID YOU MAKE THIS RECIPE?

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Recipe Rating




    54 comments
    1. Cleo Burrows
      July 13, 2021 AT 5:20 pm

      5 stars
      This are delicious and moist. I subbed out applesauce for the butter, ripe banana for the pumpkin and 3 egg whites for the 2 eggs. They were a bit dense in texture but that might be the 3/4 c mashed bananas I used. Will be making these again.

      1. Brittany Mullins
        July 14, 2021 AT 11:17 am

        Yay! So glad these muffins were a hit, even with the substitutions. Thanks for the review, Cleo! I really appreciate it!

    2. 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. 🙂

    3. 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

    4. 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.

    5. 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. 🙂

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