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…

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.

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.

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!

Want More Delicious Muffin Recipes?

• Flourless Pumpkin Muffins
• Carrot Raisin Almond Flour Muffins
• Cranberry Pecan Muffins
• Banana Oat Bran Muffins
• Blueberry Almond Muffins

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. 

Healthy Apple Cinnamon Muffins

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★★★★★

5 from 2 reviews

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

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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.

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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

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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