Healthy Apple Muffins
This post may include affiliate links. Thank you for your support.
These healthy apple muffins are made with whole wheat flour and sweetened with coconut sugar. They’re packed with fall flavor and extra moist thanks to pumpkin puree!
Every fall without fail, we end up coming home from the apple orchard with way more apples than we know what to do with. I love making my healthy apple crisp with them, but when I want something I can grab on the go all week, these healthy apple muffins are always my first move.
The secret to how moist these are is pumpkin puree. I know it sounds unexpected in an apple muffin recipe, but it keeps the crumb incredibly tender without needing a ton of butter, and it adds a subtle warmth that pairs so well with the cinnamon and fresh apple chunks. The cinnamon sugar topping is non-negotiable. It bakes into a lightly crisp, sparkly crust on top that the kids go straight for every single time!
Table of Contents
“Perfect fall muffin! Delicious, moist, and all the fall feels. Both my son and spouse love them. Thanks for the wonderful recipe.”
Why I Love This Apple Muffin Recipe
- Healthier: Unlike traditional muffins loaded with refined flour and sugar, these apple muffins are made with whole wheat flour, coconut sugar, Greek yogurt and pumpkin. They’re packed with wholesome ingredients that make for a healthier treat without sacrificing flavor.
- Perfectly Spiced: The combination of cinnamon, pumpkin and fresh apples gives these muffins the perfect fall flavor!
- Great for On-the-Go: These muffins are portable and perfect for busy mornings. Just grab one as you head out the door, and you’ve got a delicious breakfast or snack.
- Kid-Friendly: Olivia and Tucker are big fans of these muffins! I love adding them to their school lunch boxes for a healthy fall treat.
Ingredients Needed
- 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.
- cinnamon – cinnamon with apple is the ultimate fall flavor combo. You’ll also use some for the topping.
- eggs – the eggs are needed to help provide structure for the muffins so they rise and become nice and fluffy.
- coconut sugar – a less processed alternative to brown sugar with a subtle caramel flavor that pairs perfectly with the apples and cinnamon. You will use it in both the batter and the topping.
- butter – just four tablespoons keeps these muffins rich and tender. Make sure it is fully softened before mixing or it will not incorporate properly into the batter.
- 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.
- Greek yogurt – I typically use plain full-fat or low-fat Greek yogurt, which helps keep these muffins moist. No dry muffins here!
- apple – the star of the show! You’ll need about 1-2 apples, peeled and finely chopped into pieces. I typically use Honeycrisp or Pink Lady apples, depending on what I can find.
Find the full ingredient list with measurements in the recipe card below.
Recipe Substitutions
- Flour: If you don’t have whole wheat flour on hand, you can use all-purpose flour.
- Pumpkin: Don’t have pumpkin on hand or want to amp up the apple flavor? You can substitute the pumpkin with applesauce, instead!
- Coconut sugar: You can use brown sugar if that’s what you have on hand.
- Want to make them vegan? Use two flaxseed eggs instead of regular eggs, vegan butter instead of real deal butter and non-dairy yogurt instead of regular Greek yogurt.
How to Make Healthy Apple Muffins
Step 1: In a small bowl mix together your cinnamon and sugar topping. Set aside.
Step 2: Add all the dry ingredients to a large mixing bowl and mix to combine.
Step 3: Add all wet ingredients to a separate bowl. Whisk to fully combine.
Step 4: Gently fold the dry ingredients into the wet ingredients. Then stir in the apples chunks.
Step 5: Pour the batter into the prepared muffin pan and sprinkle with the cinnamon sugar topping.
Step 6: Bake for 22-25 minutes or until a toothpick inserted into the center of a muffin comes out clean.
Brittany’s Tips!
- Do not overmix the batter: Stir the wet and dry ingredients together until just combined, even if there are a few small streaks of flour remaining. Overmixing develops the gluten in the flour and leads to dense, tough muffins instead of light and fluffy ones.
- Make sure your butter is fully softened: Cold butter will not mix properly into the batter and can leave lumps. Pull it out of the fridge at least 30 minutes before you start baking.
- Use the toothpick test: Start checking at the 22-minute mark. Insert a toothpick into the center of a muffin and if it comes out clean or with just a few dry crumbs, they are done. A few moist crumbs are fine but wet batter means they need more time.
- Cool completely before storing: I cannot stress this enough. Putting warm muffins into a container traps steam and creates condensation which leads to soggy muffins. Let them cool fully on a wire rack first.
How to Store Apple Muffins
Let the muffins cool completely on a wire rack before storing. They will keep at room temperature for 2 to 3 days, in the fridge for up to one week, or in the freezer for up to 3 months. I actually prefer these straight from the fridge, the texture firms up slightly and they taste amazing cold.
To freeze, let them cool completely then transfer to a freezer-safe bag. Thaw overnight in the fridge or reheat in the microwave for 30 to 60 seconds.
Frequently Asked Questions
I reach for Honeycrisp or Pink Lady for their sweetness and firm texture. They hold up well when baked and do not turn mushy inside the muffin. Fuji and Gala are also great options. I would avoid Red Delicious since they tend to be too soft and mealy when baked.
Not really. The pumpkin is subtle and mostly acts as a moisture booster rather than a dominant flavor. The apple and cinnamon are what you taste most. If you are on the fence about it, just try it once. I promise you will not regret it.
I recommend peeling them for the best texture. Apple skins can become chewy and tough once baked which is not what you want in a tender muffin.
More Muffin Recipes to Try
If you enjoyed this recipe, please consider leaving a ⭐ star rating and let me know how it went in the 📝 comments below.
Healthy Apple Muffins
Ingredients
- 2 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 full-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, mix together the topping – 2 Tablespoons of sugar with 1 teaspoon cinnamon. Set aside2 Tablespoons coconut sugar or dark brown sugar, 1 teaspoon cinnamon
- In a medium bowl, stir together the flour, baking soda, baking powder, cinnamon and salt.2 cups whole wheat flour, 1 teaspoon baking powder, 1 teaspoon baking soda, ½ teaspoon cinnamon, ¼ teaspoon sea salt
- In a large bowl, mix the ¾ cup sugar with the softened butter until combined. Add the eggs, pumpkin and vanilla. Stir in yogurt.2 eggs, ¾ cup coconut sugar, 4 Tablespoons butter, ¾ cup canned pumpkin or homemade pumpkin puree, 1 teaspoon vanilla, ¾ cup plain full-fat Greek yogurt
- Add the flour mixture to the wet mixture and gently stir until just combined. Don't overmix! Gently stir in the apple chunks.1 ½ cups peeled and finely chopped apple pieces
- Scoop the batter into the prepared muffin pan, dividing evenly between 12 muffin cups. Sprinkle with the cinnamon sugar topping. Bake for 22-25 minutes or until a wooden pick inserted in the center of a muffin comes out clean.
- Let cool on a wire rack for 15 minutes.
Video
Notes
- I highly recommend using silicone or paper liners for these muffins! These make for easy removal and less mess. If you don’t have liners, make sure to thoroughly grease the muffin tins. These are my favorite silicone muffin cups.
- Store leftover muffins at room temperature for 2-3 days, in the refrigerator for up to 1 week or in the freezer for up to 3 months.
Nutrition
Nutrition information is automatically calculated, so should only be used as an approximation.
Like This Recipe? Rate & Comment Below!
Love the idea of healthy apple muffins! They’re a great way to enjoy a sweet treat without compromising on nutrition. Thanks for sharing this yummy and wholesome recipe.
Of course! Hope you enjoy!
These are so delicious! My husband normally hates baked goods with whole wheat flour but he’s been wolfing them down
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!
Can you use whole wheat pastry flour?
Totally! That should work fine. Let me know if you end up making these and how they turn out!
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 😍
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!
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.
Oh no!! So sorry to hear that, Lindsay. Did you change anything about the recipe?
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!!
Sorry about the confusion! You can use either flour or a combo of the two, but I just updated the instructions. 🙂
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!
Woo!! So happy these muffins were a success, Joleen! Thanks for the review. I really appreciate it!
Perfect fall muffin! Delicious, moist, and all the fall feels. Both my son and spouse love them. Thanks for the wonderful recipe.
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!
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.
Yay! So glad these muffins were a hit, even with the substitutions. Thanks for the review, Cleo! I really appreciate it!
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.
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. 🙂