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 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 32 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 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
Course: Breakfast
Cuisine: American
Keyword: healthy apple muffins

DID YOU MAKE THIS RECIPE?

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Recipe Rating




    64 comments
    1. Phoebe
      December 14, 2021 AT 5:13 pm

      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. Brittany Mullins
        December 15, 2021 AT 10:40 am

        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!

    2. Lindsay Maielli
      October 19, 2021 AT 11:28 pm

      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.

      1. Brittany Mullins
        October 22, 2021 AT 4:41 pm

        Oh no!! So sorry to hear that, Lindsay. Did you change anything about the recipe?

    3. Lindsay F
      October 10, 2021 AT 11:23 pm

      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. Brittany Mullins
        October 11, 2021 AT 5:59 pm

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

    4. Joleen B
      October 10, 2021 AT 7:12 am

      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!

      1. Brittany Mullins
        October 12, 2021 AT 10:31 am

        Woo!! So happy these muffins were a success, Joleen! Thanks for the review. I really appreciate it!

    5. Samantha
      September 28, 2021 AT 1:41 pm

      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. Brittany Mullins
        September 29, 2021 AT 10:39 am

        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!

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