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!
Almost every fall we go apple picking at a local orchard and bring home a ton of apples! I love eating apples with my date caramel sauce or making apple nachos for a quick and healthy snack, but I also love making delicious baked good with fresh apples too. I love making my vegan apple bread and baked apple cider donuts, but these healthy apple muffins are usually my go-to apple recipe!
These muffins are hearty, moist and have the perfect amount of sweetness from the coconut sugar and apple chunks. As with most muffins, they pair great with a cup of coffee like my pumpkin spice latte on a chilly fall morning.
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Why You’ll Love These Muffins
- 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 – 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.
- 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 gluten-free? 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.
- 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 Tip!
Use 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.
How to Store Apple Muffins
Let these muffins cool completely before storing them. I recommend storing them in the fridge rather than on your countertop. They’ll last longer and they taste delicious straight from the fridge.
That said, these muffins will last 2-3 days at room temperature, up to one week in the fridge or up to 3 months in the freezer.
Brittany’s Tip!
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!
Frequently Asked Questions
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, Fuji and Granny Smith are fantastic apples to bake with.
Definitely! These muffins store really well in the freezer. Just let them cool completely then transfer them to an airtight freezer-safe container or bag for storage. They can be stored in the freezer for up to 3 months. To thaw, place them in the fridge overnight.
No! This is totally a personal preference. I typically don’t peel the apples when making these muffins, but if the skin doesn’t bother you then you can totally skip peeling the apples, which will save time! Once the apples are cooked the skin will soften so it’s hardly noticeable.
More Muffin Recipes
Be sure to check out all of my apple recipes as well as the full collection of muffin recipes here on EBF!
If you enjoyed this recipe, please consider leaving a ⭐ star rating and let me know how it went in the 📝 comments below.
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Preheat oven to 350°F. Line a muffin pan with cupcake liners or coat with cooking spray.
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In a small bowl, mix together the topping – 2 Tablespoons of sugar with 1 teaspoon cinnamon. Set aside
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In a medium bowl, stir together the flour, baking soda, baking powder, cinnamon and salt.
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In a large bowl, mix the ¾ cup sugar with the softened butter until combined. Add the eggs, pumpkin and vanilla. Stir in yogurt.
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Fold the flour mixture into the wet mixture. Gently stir in the apple chunks.
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Pour the batter into the prepared muffin pan and sprinkle with the brown sugar topping. Bake for 22-25 minutes or until a wooden pick inserted in center of 1 of the muffins comes out clean.
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Let cool on a wire rack for 15 minutes.
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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.
- 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 gluten-free? 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.
- 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.
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.