These Healthy Apple Muffins are soft and moist, perfectly spiced, and topped with an easy crumb topping.
author’s note
The Muffins My Kids Think Are Dessert!
Every fall, we kick off the season with a family apple-picking trip. It’s become one of my favorite traditions. We always come home with way more apples than I planned for, but I never worry about using them up.
Between these healthy apple muffins, apple pie, and my go-to apple chicken salad, I fly through them.
These Apple Muffins were inspired by bakery-style muffins but made with better ingredients. They still have that same flavor, moisture, and texture you’d expect, but they’re a little more feel-good. I love that my kids think they’re getting a treat, but they’re actually perfect for breakfast or a snack that keeps them full and happy.
Featured Comment
“These muffins turned out great! Really nice and soft. Not dense like many of the other healthier muffins I have tried! Good flavor… I will definitely be making these again. Thanks for the great recipe!”
– Ross
Ingredients For Healthy Apple Muffins
- Flour: Use plain white for regular muffins, or white whole wheat.
- Cornstarch: This gives the muffins a soft texture, mimicking cake flour.
- Baking powder: Essential for making the batter rise.
- Spices: These muffins contain subtle amounts of cinnamon, nutmeg, and allspice. Adjust to taste or add apple pie spice.
- Vanilla Greek yogurt: Opt for full-fat, flavorful Greek yogurt. I prefer Greek God’s® Honey Vanilla.
- Apple and lemon juice: Use finely diced, peeled Granny Smith apples. Lemon juice adds zest and prevents apple browning.
Quick Tip
Which apples are best for baking? For baking, choose apples that retain structure to avoid mushiness. Granny Smith is ideal for its sweet-tart balance. Other good options include Honeycrisp, Jonagold, Braeburn, and Pink Lady.
How To Make Healthy Apple Muffins
- Prep: Preheat oven to 350°F. Grease/flour 8 muffin cavities. No liners.
- Dry Mix: Combine flour, cornstarch, baking powder, and spices.
- Wet Mix: Whisk egg, yogurt, coconut oil, vanilla, and brown sugar.
- Apple: Mix diced apple with lemon juice; add to dry ingredients.
- Combine & Fill: Mix wet into dry. Fill muffin cavities 3/4 full. Add water to empty spots.
- Topping: Mix topping ingredients; sprinkle on apple muffins. Bake for 20-23 mins
Tips For Success
- Spoon and level the flour to ensure moist, soft muffins.
- Measure ingredients accurately; a food scale is ideal. Here’s the one I use.
- Avoid over-mixing the batter to prevent muffins from sinking in the center.
- Use finely chopped apples, not grated, to prevent excess moisture.
Storage
Store cooled healthy apple muffins in an airtight container at room temp for 2–3 days or in the fridge for up to 3 days.
To freeze, wrap cooled muffins and store in a freezer-safe bag for up to 3 months; thaw at room temp or microwave to reheat.
More Apple Recipes:
Desserts
Applesauce Bread
Desserts
Apple Cheesecake Bars
Salads
Apple Salad Recipe
Desserts
Apple Turnover Recipe
Homemade Healthy Apple Muffins
Equipment
Ingredients
- Cooking spray
- 1 cup all-purpose flour or whole wheat flour
- 1 tablespoon cornstarch
- 1-1/2 teaspoons baking powder
- 1/2 teaspoon salt
- 1/2 teaspoon ground cinnamon
- 1/4 teaspoon ground nutmeg see note 1
- 1/4 teaspoon allspice
- 1 large egg
- 1/2 cup honey vanilla Greek yogurt
- 1/4 cup coconut oil melted, see note 2
- 1/2 teaspoon vanilla extract
- 1/2 cup light brown sugar lightly packed
- 1 cup peeled and finely diced apple
- 1/2 teaspoon lemon juice
- 3 tablespoons all-purpose flour or whole wheat flour
- 2 tablespoons quick oats
- 1/2 teaspoon ground cinnamon
- 3 tablespoons brown sugar not packed
- 2 tablespoons melted coconut oil see note 2
Instructions
- Preheat oven to 350°F (175°C). Generously coat a muffin pan with cooking spray. Measure and set out your egg and yogurt to reach room temperature. Melt coconut oil, measure, and set aside to reach room temperature.
- In a large bowl, add the muffin dry ingredients—flour (use a food scale if you have it—135g), cornstarch, baking powder, salt, cinnamon, nutmeg, and allspice. Mix until combined.
- In a separate bowl, whisk together the muffin wet ingredients—egg, Greek yogurt, melted coconut oil (see note 2), vanilla extract, and brown sugar. Whisk together until smooth.
- Peel and very finely chop the apple. Toss with the lemon juice. Add to the dry ingredients and stir until the apple pieces are coated in flour.
- Add dry ingredients on top of wet. Mix with a spatula until ingredients are combined and no dry streaks of flour remain.
- Use a 1/4 cup measuring cup to scoop the batter into each of the sprayed muffin cups. There should be enough batter for about 10 muffins.
- In another bowl, toss together the Cinnamon Sugar Topping dry ingredients—flour, quick oats, cinnamon, and brown sugar. Pour in the coconut oil and mix to combine, crumble with your fingertips if needed. If the mixture is too wet, add flour; if it’s too dry, add coconut oil. Sprinkle this topping evenly on top of each muffin. Don’t press the topping into the muffin.
- Bake for 20–25 minutes or until a toothpick when inserted in the center of the muffin comes out clean. Remove the pan from oven and allow to cool for 5 minutes before taking the muffins from the tin. Use a spoon or butterknife to trace around the edges and coax the muffins out. Allow muffins to finish cooling on a cooling rack so the bottoms don’t get soggy. Enjoy warm!
Recipe Notes
Nutrition
Nutrition information is automatically calculated, so should only be used as an approximation.
Does anyone have the nutrition facts on these? Thank you!
Found this recipe on pinterest and made ’em, can’t describe how delicious they are. Possibly one of the best recipes I’ve found in a while!
That is so great to hear! 🙂 I’m glad you enjoyed these!!
These muffins turned out great! Really nice and soft. Not dense like many of the other healthier muffins I have tried! Good flavor but I would probably increase the amount of cinnamon….but thats just my taste. I will definitely be making these again. Thanks for the great recipe!
Awesome!! SO great to hear! I’m glad you enjoyed these Ross! 🙂
I made these and I loved them. I used plain Greek yogurt because it’s what I had on hand. However, as awesome as they are that way, I am sure using apple pie Greek yogurt will be even better…if that’s even possible
Haha!! Thanks so much for your sweet comment Mary! So glad you enjoyed these 🙂
These muffins are awesome! If I could give these more than 5 stars I would! I made them last night and put them in the freezer. Pop them in the microwave for 45 seconds and they are perfect. I just ate two of them and could probably eat the whole rest of the batch. The batter was very thick, so I was not expecting them to be so light and fluffy with a lovely crispy top and edges. I used AP flour, 1/3c brown sugar, and one 5.3oz nonfat apple pie greek yogurt in the muffin part; for topping used 1 1/2T butter, 2T quick oats, 1/2t cinn, about 1 1/2T brown/dk brn sugar, about 2T flour (started w/1T and added until right consistency). Thanks for another awesome muffin recipe and for the healthy swaps, keep ’em comin’!
You are so sweet Robin!! I so appreciate your kind comments and trying so many recipes!! So glad you enjoyed these muffins 🙂 And your crisp topping sounds amazing!!
Just made these substituting King Arthur gluten free flour for my mom who is celiac! They were AWESOME!
Yeah!! So great to hear 🙂 Thanks for the comment!
Can I make these without the coconut oil?
I would not recommend leaving out the coconut oil, but you could try a different oil in place of coconut such as canola or vegetable oil. I haven’t tried either one so I can’t say for sure if the taste or texture will be different but better than leaving out that ingredient entirely!
I am so amazed at how well this recipe turned out! I’ve tried so many different types of healthier muffins in the past and they were never quite right, but these were perfect! My kids just started school this week and breakfast is always a struggle. They don’t like cereal (especially when I won’t buy the high sugar kinds) they don’t like toast, eggos, granola bars, eggs, or most typical quick breakfast options….so we made muffins. These were fluffy, delicious, the topping adds just a little sweetness without going overboard. Now, I just need to go find this “white wheat flour” I keep reading about so my next batch will have more fiber.
P.S. I’m trying to rate your recipe 5 stars, but for some reason, it’s not working for me.
Aw thank you so much Jenny!! What a sweet comment! 🙂 So glad to hear your kids enjoyed them!
Love these pictures Chelsea!
I am so ready for fall! I can’t wait for all things pumpkin, cinnamon, and such. These muffins look amazing, pinning right away! Thanks for sharing.