Healthy Apple Cookie Cups Recipe

For a fun twist on a classic apple crisp try this healthy apple cookie cups recipe! They combine crisp oatmeal cookies with homemade apple pie filling for the perfect healthy fall treat. Gluten-free, dairy-free, and refined sugar-free!

Imagine warm, soft cooked apples with a good dose of cinnamon and some maple syrup. All of that, in crispy oatmeal cookie cups. If you like all things apple pie, apple crumble, apple crisp, and love cinnamon then this cookie cups recipe will be your new obsession!

The best part is that these apple pie cookie cups are not even bad for you (as far as treats can go!). They taste like decadent little treats for sure, but are only sweetened with unprocessed nutritious ingredients like coconut sugar and maple syrup! Instead of butter, these are made with coconut oil to keep these babies dairy-free.

But honestly, health benefits and simplicity aside, my favorite part about these is the way they make your kitchen smell while baking. So delicious and comforting! Fall central!

I mean, on a dull and rainy day making these apple crisp cookie cups is an easy way to instantly lift your mood. That’s what I love about fall and holiday baking, it makes you feel all cozy!

But honestly, I make this cookie cups recipe all year long because there’s no bad time for apple pie anything, ever. Don't you think? However, you can totally use a mix of different fruit, like apples and pears or peaches. Just reduce the cooking times if you use softer fruit.

Want some raisins or cranberries in there? That would taste amazing, too!

How to make Healthy Apple Crisp Cookie Cups:

Step 1 - In a large mixing bowl, whisk together oats, almond flour, arrowroot starch, coconut sugar, sea salt, and baking soda. Stir until well combined.

Step 2 & 3  - In another small bowl, whisk together the egg, coconut oil and vanilla. Add to dry mixture and stir until well combined.

Step 4 - Grease a standard muffin pan with a bit of coconut oil or cooking spray. Roll the dough into 12 equal balls, and add to the muffin pan. Chill for 15-20 minutes in the fridge. While the dough is chilling, preheat oven to 350F/ 175C degrees.

Step 5 - Flatten the balls in the muffin tins then shape them into cups using a shot glass (or something of similar sizes like a salt grinder or shaker), pressing dough’s center.

Step 6 - Once all dough is shaped, bake them for 13-15 minutes or until golden brown. After 5-7 minutes of baking, remove pan from the oven and reinforce the “cups” using the same shot glass (it might look like the hole has almost disappeared, it’s normal). Finish baking and right after taking them out of the oven, reinforce the cups one last time.

Let cool for 20 minutes and pop the cups out of the pan (you might need to run a thin knife around the edges to help them pop out). Place the apple crisp cookie cups on a cooling rack or serving platter.

Step 7 - While the cups are cooling, make the filling. Sautee coconut oil and diced apples over medium-high heat, stirring ofte. Once apples begin to soften, add maple, water, vanilla, spices, and salt.

Step 8 & 9- Continue stirring often over medium heat until apples are tender, but not mushy. Once the apples look syrupy and softened, remove from heat and divide evenly among cookie cups.

Tips:

• These cups are best served warm, within one hour.
• The cups will soften a lot on the 2nd day because of the apples and the apple filling won’t look as glossy.  They will still taste great, but if you are making them for a party I recommend serving them the same day.
• Peel the apples before cutting them into chunks. The skin doesn’t break down during baking and does not look pretty in these.
• Be sure to dice your apples evenly so that they cook evenly!

5 from 2 votes

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Healthy Apple Crisp Cookie Cups

For a fun twist on a classic apple crisp try this healthy apple cookie cups recipe! They combine crisp oatmeal cookies with homemade apple pie filling for the perfect healthy fall treat. Gluten-free, dairy-free, and refined sugar-free!

Course Breakfast, Snack

Cuisine American

Keyword apple crisp cookie cups, cookie cups, mini apple pies

Prep Time 45 minutes

Cook Time 25 minutes

Total Time 1 hour 10 minutes

Servings 12

Calories 253 kcal

Author Marie

Ingredients

Cookie cups:

• 1 ¾ cups rolled oats
• ¾ cup almond flour
• ¼ cup arrowroot starch or tapioca starch
• ¾ cup coconut sugar or brown sugar
• ¾ teaspoon sea salt
• ¼ teaspoon baking soda
• ½ cup coconut oil liquefied + more to grease
• 1 large egg
• 2 teaspoons vanilla extract

Apple Filling

• 2 teaspoons coconut oil
• 3 cups apples peeled and cut into small cubes (about 3 medium apples or 2 large)
• ¼ cup maple syrup
• ¼ cup water
• 1 teaspoon vanilla extract
• 1 teaspoon cinnamon
• ⅛ teaspoon nutmeg
• ¾ teaspoon sea salt

Instructions

Cookie Cups

1. In a large mixing bowl, whisk together oats, almond flour, arrowroot starch, coconut sugar, sea salt, and baking soda. Stir until well combined.
2. In another small bowl, whisk together the egg, coconut oil and vanilla. Add to dry mixture and stir until well combined.
3. Grease a standard muffin pan with a bit of coconut oil or cooking spray. Roll the dough into 12 equal balls, and add to the muffin pan. Chill for 15-20 minutes in the fridge.
4. While the dough is chilling, preheat oven to 350F/ 175C degrees.
5. Flatten the balls in the muffin tins then shape them into cups using a shot glass (or something of similar size like a salt grinder or shaker), pressing dough’s center.
6. Once all dough is shaped, bake them for 13-15 minutes or until golden brown. After 5-7 minutes of baking, remove pan from the oven and reinforce the “cups” using the same shot glass (it might look like the hole has almost disappeared, it’s normal). Finish baking and right after taking them out of the oven, reinforce the cups one last time.
7. Let cool for 20 minutes and pop the cups out of the pan (you might need to run a thin knife around the edges to help them pop out). Place them of a cooling right or serving platter.

Apple Filling

1. While the cups are cooling, make the filling. Sautee coconut oil and diced apples over medium-high heat, stirring often.
2. Once apples begin to soften, add maple, water, vanilla, spices, and salt.
3. Continue stirring often over medium heat until apples are tender, but not mushy. Once the apples look syrupy and softened, remove from heat and divide evenly among cookie cups.
4. These cups are best served warm, within one hour (see notes).

Recipe Notes

• These cups are best served warm, within one hour.
• The cups will soften a lot on the 2nd day because of the apples and the apple filling won’t look as glossy.  They will still taste great, but if you are making them for a party I recommend serving them the same day.
• Peel the apples before cutting them into chunks. The skin doesn’t break down during baking and does not look pretty in these.
• Be sure to dice your apples evenly so that they cook evenly!

Nutrition Facts

Healthy Apple Crisp Cookie Cups

Amount Per Serving (1 cup)

Calories 253 Calories from Fat 126

% Daily Value*

Fat 14g22%

Saturated Fat 9g56%

Cholesterol 14mg5%

Sodium 340mg15%

Potassium 96mg3%

Carbohydrates 30g10%

Fiber 3g13%

Sugar 14g16%

Protein 4g8%

Vitamin A 37IU1%

Vitamin C 1mg1%

Calcium 35mg4%

Iron 1mg6%

* Percent Daily Values are based on a 2000 calorie diet.

If you tried this apple crisp cookie cups recipe, don’t forget to rate the recipe below and let me know how it went in the comments – I love hearing from you! You can also follow me on Instagram, Pinterest, and Facebook for more deliciousness and behind-the-scenes!

More recipes from the blog you will love:

• Apple Pie Granola
• Healthy Berry Crisp
• Paleo Lemon Curd Tart
• Healthy Banana Split
• Fudgy Paleo Brownies
• Almond Butter Blondies

UPDATE NOTE: This post was originally published on September 18, 2017 and republished in September 2020 with an updated recipe, new photos and more tips.