These healthy Apple Crisp Cookie Cups are easy to make and can be enjoyed as a dessert, or for breakfast! Made with almond flour, oatmeal and natural sweeteners like maple syrup and monk fruit sugar, making them gluten- free and low sugar!

❤️ Why You’ll Love This Recipe
Imagine warm, soft cooked apples with a healthy dose of cinnamon and some maple syrup. All of that bundled into a bite-sized treat, making them perfect for snacking or sharing with friends and family! If you like all things apple, cinnamon, and fall then this healthy apple pie cookie cup recipe is for you!
I think I can confidently say that apple pie is my most favorite fall flavor, so it only makes sense that these healthy apple pie cookie cups are the first recipe to kick off the fall season!
Full transparency, I live in Florida where we don’t really get the kind of fall that most think of when this time of year rolls by. Something about the slowing down and shedding of seasons feels very natural and comforting to me. Not sure about you, but I am ALL about those cozy vibes. Who isn’t?!
Really though, the reason we all love this time of year so much definitely has to do with all those fall flavors! Apples, cinnamon, pumpkin, chai, cider, caramel – they’re all so warm and welcoming. How could you not resist?
Enter these healthy apple pie cookie cups to begin the seasons festivities!
Jump to:
- ❤️ Why You’ll Love This Recipe
- 📋 Ingredients in Healthy Apple Crisp Cookie Cups Recipe
- 🥧 Apple Pie Filling Ingredients
- ⏲️ How to make Healthy Apple Crisp Cookie Cups Recipe
- 🥣 How to store Healthy Apple Crisp Cookie Cups Recipe
- 🍎 If you liked this recipe, you’ll want to try these!
- Healthy Apple Crisp Cookie Cups Recipe
📋 Ingredients in Healthy Apple Crisp Cookie Cups Recipe
The best part about apple pie recipes is that they’re generally made with easy ingredients that you most likely have at home already! These bite sized apple pies will be quite similar ingredients, but you don’t have to make a whole dough to roll out. So nice, right?

- almond flour
- gluten-free oats
- maple syrup
- monk fruit sweetener
- vanilla extract
- baking soda
- cinnamon
- salt
- egg
- ghee
🥧 Apple Pie Filling Ingredients
Homemade apple pie filling is made with fresh apples, fall spices, and a little bit of natural sugar and butter. Making this filling very similar to your standard apple pie filling, but with natural sweeteners and ghee – a clarified butter that is rich in healthy fats, making it a great alternative to help support your heart and cardiovascular system!
- apples (I like to use a combination of apples!)
- tapioca flour
- ghee
- maple syrup
- cinnamon
- salt

⏲️ How to make Healthy Apple Crisp Cookie Cups Recipe
Your traditional apple crisp usually requires quite a bit of time to make and really, who has time for that anymore? Trust me when I say that these individual apple crisp cookie cups are fast, easy and definitely don’t compromise on flavor.
First step is to make your oatmeal cookie cup crust. Forget needing to make a dough to roll out, cut, then bake. This recipe will have you toss all the dry ingredients (almond flour, oatmeal, cinnamon, baking soda, and salt) into a large bowl and mix together.
In a separate bowl, you’ll then mix together the wet ingredients (eggs, maple syrup, monk fruit sugar, vanilla extract, and ghee). Once these are well combined, you’ll add the wet ingredients into the bowl with the dry ingredients and stir until just combined.
Next, you’ll want to grease a muffin tin with a bit of olive oil spray or coconut oil. Then, scoop 2 tablespoons of dough into your muffin tin. Once the dough is evenly disbursed, you can either use your fingers or the back of a spoon to create a bit of a dent where the filling will go.
Bake for 10 minutes, or until golden brown and let cool while you make the apple pie filling.
Make the apple pie filling while the cookie cups are baking/cooling by heating a small saucepan with 1 tbsp ghee. Once heated, add the chipped apples, maple syrup and cinnamon. Stir together and let cook for 3-5 minutes, or until apples are soft. Once the apples are soft, add in the tapioca flour and salt, combine together and remove from heat.
Once the cups have cooled, divide the filling among the cups and bake again for 5 minutes or so. Allow to cool and top with icing, whip cream, ice-cream – or enjoy as is!

🥣 How to store Healthy Apple Crisp Cookie Cups Recipe
Apple pie is typically always best when served warm and fresh – I recommend you enjoying these the same way! However, they can be stored in an airtight container and left in the fridge for up to three days.
If you do decide to refrigerate, they will need to soften a bit before enjoying, so be sure to take them out maybe 15 minutes before you’d like to enjoy them and they should be good to go!
I sincerely hope you make these easy apple pie cookie cups to kick off fall and enjoy them as much as we do! Let the fall aromas commence!

🍎 If you liked this recipe, you’ll want to try these!
- Quick and Easy Peach Cobbler Oatmeal Breakfast Bake
- High Protein Coffee Cake Donuts
- Bananas Foster Banana Bread
- Blueberry Lemon Streusel Muffins
- Easy Apple Cinnamon Baked Donuts
If you make this recipe, be sure to comment below and let me know how it was! Also tag @livinginflux on Instagram and use the hashtag #livinginflux so I can see it and feature you!

Healthy Apple Crisp Cookie Cups Recipe
Ingredients
- 1 cup almond flour
- 1 cup gluten-free rolled oats
- 1 teaspoon cinnamon
- ¼ teaspoon baking soda
- ¼ teaspoon salt
- ¼ cup monk fruit sweetener
- 2 tablespoon maple syrup
- 2 eggs
- ¼ cup ghee
- 1 teaspoon vanilla extract
Apple Pie Filling
- 1 apples medium
- 1 tablespoon ghee
- 3 tablespoon maple syrup
- 1 tablespoon tapioca flour
- ½ teaspoon cinnamon
- ½ teaspoon cinnamon
- pinch of salt
Instructions
- Preheat oven to 350F
- Start by making the oatmeal cookie cups: In a large bowl, mix together the dry ingredients of almond flour, oats, cinnamon, salt and baking soda.
- In a second, slightly smaller bowl, mix together: monk fruit sugar, maple syrup, eggs, ghee, and vanilla extract.
- Gently pour the mixed wet ingredients into the larger dry ingredient bowl and combine until well incorporated.
- Taking a small ice cream scooper, spoon, or tablespoon, spoon out roughly 2 tablespoons of sough into a greased muffin tin, gentle pressing back of spoon (or fingers) in the center to create a dent where the apple pie filling will be placed. Bake for 10-12 minutes, or until lightly golden brown
- While the cookie cups are baking, prepare the apple pie filling by heating a large skillet over medium heat. Add ghee to the pan and let it melt.
- Once the ghee has melted, add chopped apples and cinnamon and allow to cook together for roughly 3 minutes, or until the apples get a bit soft.
- In the same skillet, you'll add the remaining ingredients of maple syrup, tapioca flour and a pinch of salt. Stir together and then remove from heat to allow the filling to thicken. Roughly 10 minutes or so.
- Once the cookie cups have been removed from the oven, cooled, and the apple pie filling thickened to your liking, place a heaping scoop of the filling in the dented area you created prior to baking (you may need to press this down a bit more again to get the desired amount of filling in the cup).
- Once all of the cups have been filled, bake again in preheated oven for 5 minutes.
- Remove from oven and allow to cool before enjoying. Feel free to add any topping you'd like and enjoy!





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