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.
We made these today as baked donuts–it took 13 minutes at 350. We followed the recipe but used granola in place of oatmeal for the topping because we were out. Still delicious, though! Thanks for the great recipe!
Love your idea to convert these to donuts!! Yum! 🙂
I used white whole wheat flour, vanilla Greek yogurt and canola oil. I cut the apples up very small. They muffins are a little drier than I would like. Maybe I’ll put in some shredded apple next time in addition the the chopped apple. It made 13 muffins with the yellow scoop. Took 17 min to bake at 350F.
Sorry these were drier than you’d like; the shredded apple sounds like a great idea!
Hi Chelsea, thanks for the recipe! It looks so good. I was wondering: any ideas on how to adapt the recipe to mini muffins? Thanks again!
These muffins are delicious! I shredded my apples because I was too lazy to dice them. They turned out perfectly moist, and the crunchy topping makes them even better! Thanks for the recipe!
So happy you enjoyed these! Great idea to shred the apple 🙂
Hi,
I just wanted to know what the nutritional value of these muffins are.
I use Greek yogurt so I don`t have to buy probiotics. Greek yogurt is very nutritional and healthy.
I just made a batch and OhMyGosh delicious!!! I substituted the brown sugar for dextrose powder and a bit of rice malt syrup to make it a sugar free muffin. I think the cornstarch and greek yoghurt make this a very special recipe. Even with the adjustments this is so moist and fluffy and still sweet. Great recipe thank you!
Thank you so much for your review and comment Danielle! 🙂 Glad you liked the muffins!
These muffins were amazing. I initially was concerned they would taste only like coconut. The apple flavor was wonderful, used a little more than the one-cup. Recipe is a keeper ? Thank you
So happy to hear that! 🙂 Thank you for the comment Robert!
Omg this is insane! I still can’t believe the muffins are 100% healthy.. amazingly delicious!!!! Thank you ❤
You’re welcome! 🙂
These muffins were the stars on tonight dinner! Thanks you Chelsea!
That is so great to hear! Thanks so much for the comment 🙂