A wholesome version of a fall classic! These healthy baked apples are stuffed with an oat pecan crumble, then baked until soft and fragrant. The whole house smells like fall.

Leave the guilt behind with this healthy baked apple recipe!
It's just as warm and comforting, but it's made with wholesome ingredients like almond flour, oats, and maple syrup.
What are Baked Apples?
The term baked apples is exactly what it sounds like. Apples bake until soft and juicy, typically with other ingredients like brown sugar, butter, and cinnamon.
The version we're making today is a healthy spin on whole baked apples! Tart apples are cored, stuffed with a pecan oat crumble, and baked until fragrant and soft. It's a crave-worthy treat you can feel good about!
Why You'll Love Baked Apples:
- A delicious way to use up freshly picked apples from the orchard!
- Free from gluten, dairy, and animal products! Leave out the pecans and it's nut-free.
- Made with 8 wholesome ingredients. Swap the brown sugar with coconut sugar and this recipe is refined-sugar-free.
- Tastes like a healthy apple crisp! Top with whipped cream, ice cream, or vanilla Greek yogurt for a healthy-ish dessert.
Key Ingredients:
Apples - You need 4 large tart apples. I used Pink Ladies, but Honeycrisp work great too!
Quick cooking oats - I haven't tested this recipe with whole oats, but they should work too. Quick-cooking oats act more like flour and taste less chewy.
Almond flour - Almond flour is rich in nutrients, including monounsaturated fats, protein, dietary fiber, manganese, and vitamin E! I buy a big bag at Costco and use it in healthy desserts like this one.
Maple syrup - For a sweet, maple flavor! If you don't have it, you can substitute it with coconut or brown sugar.
Brown sugar - Feel free to swap the brown sugar with coconut sugar for a refined-sugar-free version. I like the taste of brown sugar so I added one tablespoon! For a sweeter filling, use two tablespoons.
Pecans - For a nutty crunch!
Coconut oil - Moistens the crumb topping and binds it together! If you don't have coconut oil, butter should work too.
How to Core the Apples:
For whole baked apples, you need to remove the core. Apple seeds are poisonous, plus you need room to add the oat filling!
- Use a large spoon to make a circle around the stem. Scoop the top off with the spoon. Alternatively, you can use a sharp paring knife.
- Use a sharp paring knife to cut around the core.
- Switch to a smaller spoon. Use the small spoon to scoop out the core and seeds, sort of like scooping the goop out of a pumpkin.
How to Make Baked Apples:
These healthy cooked apples are a breeze to make! Here's a breakdown of the recipe:
- Preheat your oven and core the apples (like shown above). The oven should be set to 350 degrees. Don't set it higher. Almond flour browns quicker than regular flour.
- Make the crumb topping. In a medium bowl, combine the almond flour, oats, pecans, brown sugar, and cinnamon. Stir, then add the maple syrup and coconut oil. Mix until a crumble forms.
- Stuff the apples. Place the cored apples on a parchment-lined sheet pan. Brush the edges with coconut oil so they don't dry out. Stuff each apple with a quarter of the filling.
- Bake the apples until they're fork-tender and soft, about 35 to 40 minutes. If the apples aren't soft enough for you, add a few more minutes. It's that easy!
The Best Apples to Use:
The best apples to use are large apples (more room for filling!) with a firm flesh that won't fall apart or get mushy. I prefer tart varieties like Pink Lady, Honeycrisp, or Granny Smith, but Fujis also work!
I'd avoid red delicious, golden delicious, or gala apples. They get too mushy when baked!
Substitutions & Variations:
- Nuts - Swap the pecans with chopped walnuts, slivered almonds, or chopped pistachios. Or for a nut-free version, omit the pecans.
- Sweetener - You can swap the maple syrup and brown sugar with a brown sugar substitute if you prefer a sugar-free version. Or swap the brown sugar with coconut sugar for no refined sugar.
- Mix-ins - Add raisins or dried cranberries for more chewy sweetness!
- Gluten-free - Make sure to use gluten-free certified oats if you have celiac disease.
- Texture - The longer you bake the apples, the softer they will be! You can check the softness with a fork.
Storage Tips:
- Serve baked apples warm! You can top them with ice cream or caramel sauce for a decadent dessert.
- Store them in an airtight container in the refrigerator for up to 2 days.
- Baked apples are NOT freezer-friendly. They are too mushy when thawed.
Make-Ahead Instructions:
While I don't recommend making the apples ahead of time, you can make the filling!
- Make the crumb topping. Combine the ingredients in a large bowl (as directed above) and mix with your hands until a crumble forms.
- Cover and chill for up to 3 days. You can cover the bowl you made it in or transfer it to an airtight container.
Then all you have to do is core and stuff the apples when you're ready. One less step!
FAQs:
How long does it take to cook an apple in the oven?
It depends on the size of the apple! If using smaller apples, they may only need 30 minutes. I used large apples and they needed 35 to 40 minutes to reach a soft, fork-tender texture.
More Apple Recipes:
Healthy Baked Apples
Equipment
- baker's half sheet pan
- Medium bowl
Ingredients
- 4 large Honeycrisp apples
- ¼ cup coconut oil plus more for brushing
- ½ cup almond flour
- ½ cup quick-cooking oats
- ⅓ cup chopped roasted pecans
- ½ teaspoon ground cinnamon
- 2 tablespoons maple syrup
- 1 tablespoon brown sugar or coconut sugar, Note 1
Instructions
- Preheat oven to 350 degrees Fahrenheit. Line a small sheet pan with parchment paper.
- Use a large spoon to scoop the top off each apple. Make a large circle around the stem and scoop it off.
- Now use a smaller spoon to scoop out the seeds and core, like scooping out the inside of a pumpkin.
- Throw the seeds and core away. Place the cored apples on the prepared sheet pan. Brush each apple with melted coconut oil.
- In a medium bowl, combine the almond flour, brown sugar, cinnamon, quick-cooking oats, and chopped pecans. Stir to combine.
- Add the maple syrup and coconut oil. Use a large spoon or your hands to mix well until a crumble forms.
- Divide the crumble between the apples, using clean hands to push the crumble down into the middle of each apple.
- Remove any excess crumble from the sheet pan.
- Bake the apples on the middle rack until soft, about 35 to 40 minutes. If the topping gets too brown, you can loosely cover it with foil.
- Carefully remove the apples from the oven and enjoy warm!
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