Healthy Apple Cinnamon Muffins

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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 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

Be sure to check out all of my apple recipes as well as the full collection of muffin recipes here on EBF!

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3.84 from 36 votes

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!
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 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 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

Nutrition information is automatically calculated, so should only be used as an approximation.

Additional Info

Course: Breakfast
Cuisine: American
Keyword: healthy apple muffins
Did you make this recipe?Mention @eatingbirdfood and tag #eatingbirdfood!

About Brittany

Hey there, I’m Brittany, the creator of Eating Bird Food, cookbook author, health coach and mama of two littles. Here you’ll find quick and easy recipes that make healthy fun and enjoyable for you and your family!

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Recipe Rating




68 Comments

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

  3. 5 stars
    Perfect fall muffin! Delicious, moist, and all the fall feels. Both my son and spouse love them. Thanks for the wonderful recipe.

    1. Aw yay! So pumped these muffins were a success, Samantha! Thanks for making them and for the review + star rating. It means the world to me!

  4. 5 stars
    Made these yesterday for a ladies book study. Not only was I impressed, but my daughter, and 4 other people. Look forward to trying other recipes from your site. Healthy doesn’t have to be boring!

  5. Hi there, quick question-the instructions say to add the all purpose flour AND whole wheat flour but the ingredients list only includes measurements for the whole wheat flour. What is the correct measurements for flour? Thanks!!

    1. Sorry about the confusion! You can use either flour or a combo of the two, but I just updated the instructions. 🙂

  6. 3 stars
    I’ve been meaning to make these since I saw them in IG (I’m a big EBF fan!) and finally did tonight. I’m bummed that these were not my favorite. The batter came out very thick and the overall texture of the cooked muffins are very spongy and they really stuck to the liners at the bottom. Maybe if I try them with real eggs and no liners they’ll be better? The flavor and nutritional value are good though.

  7. 5 stars
    These are the BEST muffins I have ever made!!! Seriously delicious and moist, the flavours are so autumnal/wintery and cosy and they were so easy to make! For substitutes I did some of my he ones recommended based on what I had available and used 2 eggs, only plain flour, and used the apple sauce recipe linked instead of pumpkin purée! Thank you for this recipe 😍

    1. Yay!! So happy to hear this muffins were a hit and that the substitutions worked out for you! Thanks so much for the review, Phoebe. I really appreciate it!

    1. Woo!! So pumped to hear these muffins were a hit. Thanks for making them and for coming back to leave a review. I so appreciate it!

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