This Healthy Apple Muffin Recipe is 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 this healthy apple muffin recipe, 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.
Healthy Apple Muffin Recipe Ingredients
| Ingredient | Tips & Easy Swaps |
|---|---|
| Apples | Granny Smith adds a nice tart flavor, but Honeycrisp, Pink Lady, Braeburn, or Jonagold all work beautifully. Dice them very small so they soften evenly while baking. |
| Greek Yogurt | Use full-fat, flavorful Greek yogurt. I prefer Greek God’s Honey Vanilla. |
| Flour | Use plain white for regular muffins, or white whole wheat. |
| Coconut Oil | Melt it first, then let it cool before mixing it into the batter. Neutral oil or melted butter also work well. |
| Warm Spices | Want even more spice? Add some apple pie spice or add an extra pinch of cinnamon. |
How To Make This Healthy Apple Muffin Recipe
- 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
chelsea’s recipe tip
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 in this healthy apple muffin recipe.
Storage
Store this cooled healthy apple muffin recipe 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:
Healthy Apple Muffin Recipe
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.
This is a quick and healthy dessert for my kids and they absolutely love it.
So happy to hear that! Thanks for the comment 🙂
Delicious thank you Chelsea! I used spelt flour and a combo of coconut oil and ghee and put it together in the Thermomix. All of us, inc my 6 and 5 yr old really enjoyed them.
I love hearing that! Thanks so much for the comment Sasha 🙂
So delicious! I made them this morning and doubled the recipe. I did one cup apples and one cup shredded carrots! I also skipped the topping. Some of the bottoms were a bit soggy- but that is my fault for adding too much water lol!!! I ate three!
So happy you liked these!! And the carrots sound like a delicious addition 🙂
Thanks Chelsea for the recipe. The muffins tasted so yummy and moist. I substituted the yogurt with milk kefir .
I’m so happy to hear you enjoyed these! Thanks for the comment 🙂
What a great recipe! I decided to see if this would work as a quick bread rather than muffins. No change to the ingredients, but baked it in a loaf pan at 325 for 40 minutes and tented the top with tinfoil for the first 20 minutes so the topping wouldn’t overcook – perfect! Your cornstarch substitution is genius.
Thank you so much Erin! I’m thrilled this worked well in a quick bread and thank you for sharing! 🙂
I try a lot of random recipes online and this is first I’m printing out because I don’t want to lose it! Used gluten free flour, only 1/4 cup sugar, plain yogurt, and no topping and they are perfectly soft and tasty!
Wow! What a compliment! 🙂 I am so thrilled these were a hit! Thank you Amy!
Just made these and they are UNREAL! So light and fluffy. Thank you for being so detailed in your instructions. It helped me so much. I used avocado oil instead of coconut oil and used plain Greek yogurt. I used a half cup of brown sugar but I will probably use a bit less next time to try to make them even healthier. Do you know the calorie/muffin on the recipe approximately?
Awe thank you so much Mandy! I’m thrilled to hear your results 🙂 And your substitutions sound delicious as well! I don’t have the calorie counts unfortunately on this recipe, but I believe My Fitness Pal would give you the most accurate count 🙂
Hi, I found your recipe on Pinterest. Subbed in whole wheat pastry flour, 1/4 cup maple syrup for the brown sugar, and used 1-1/2 cups of apples (because I misread the directions, oops!). I omitted the topping also. Despite the substitutions my husband said the muffins were great! Thanks for posting the recipe 🙂
I’m so happy they worked out well and the maple syrup in these sounds delicious! You are welcome for the recipe! Thanks for the comment Alison 🙂
Hey! I’m not a big fan of using sugars and like to use honey instead. Do you think that would work? How much do you think?
I’m not sure how you would replace the sugars with honey since I haven’t tried that in this recipe. I’m guessing it would be a bit more dense and not have the rise that these do. And I’m sorry, I couldn’t suggest an amount to use without further recipe testing since I don’t want to say something that might not have stellar results.
happy, this comes out very nice… i don’t have coconut oil so used corn oil instead… the crust part is a bit different, maybe too wet… and the sugar become “rocky” rather than like a crispy crumb… maybe i should get myself some right ingredients 🙂 thanks for the recipe.
I’m glad you enjoyed these! And yes I think the crust part will come out much better when you try the coconut oil 🙂 Thanks for the comment!