Healthy Apple Cinnamon Muffins
Published Sep 25, 2019, Updated Nov 04, 2022
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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.
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.
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!
- 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.
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.
Want More Delicious Muffin Recipes?
- Apple Yogurt Muffins
- Flourless Pumpkin Muffins
- Carrot Raisin Almond Flour Muffins
- Cranberry Pecan Muffins
- Banana Oat Bran Muffins
- Healthy Zucchini Muffins
- Almond Flour Muffins
- Pumpkin Bran Muffins
More Apple Recipes
- Healthy Apple Butter
- Apple Granola Bars
- Vegan Apple Bread
- Apple Baked Steel Cut Oatmeal
- Apple Pie Energy Balls
- Raw Mini Apple Pies
- Apple Cake
- Healthy Dutch Apple Pie
Healthy Apple Cinnamon Muffins
- 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
- 2 Tablespoons coconut sugar or dark brown sugar
- 1 teaspoon cinnamon
- 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.
- 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 information is automatically calculated, so should only be used as an approximation.