Healthy Apple Muffins

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!

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.

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.

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