Apple Crisp Cookie Cups

These apple crisp cookie cups have all the cozy flavors of apple pie in a fun, bite-sized treat. Warm cinnamon apples fill soft, buttery sugar cookie cups for the perfect mix of gooey and crisp. They’re easy to make with store-bought dough and just the right size for parties, Thanksgiving, or a cozy fall night in.

Very close up side view of a sugar cookie cup full of gooey apple filling drizzling out the side on a plate next to a cinnamon stick.

Why We Love Apple Crisp Cookie Cups

Perfect Make-Ahead Dessert – Bake the cups and prep the filling, then assemble right before serving. You still get that fresh-baked feel without the last-minute stress.
Cozy Apple Crisp Flavor – Gooey cinnamon apples meet buttery cookie cups for the ultimate fall bite in dessert form.
Quick Semi-Homemade Shortcut – Store-bought sugar cookie dough makes prep easy, even with kids helping in the kitchen.
Bite-Sized for Sharing – Perfect for fall parties, Thanksgiving dessert tables, or an easy treat after apple picking. They also are really great with my chocolate chip pecan pie bites

Love gooey cinnamon apple desserts? My sweet apple crisp dessert pizza is always fun with the kids, or these caramel apple cheesecake bars always get rave reviews! Or for a really easy dessert, try this buttery caramel apple dump cake warm!

Ingredients For Apple Crisp Cookie Cups

Find the full printable recipe with specific measurements and directions below in the recipe card.

apples I used Granny Smith apples, but you can use any baking apple
white granulated sugar – I’ve used sugar in the raw which is why it is slightly tan, but any white sugar works.
brown sugar
cinnamon – swap pumpkin pie spice or an apple pie spice blend for both the cinnamon and the nutmeg
nutmeg
cornstarch
butter – salted butter works great, mix 1/4 teaspoon of salt into the butter as the butter melts if you have unsalted butter
water
sugar cookie dough I used refrigerated dough from the grocery store. You could also use a homemade sugar cookie dough, but I would suggest making a half batch

How To Make Apple Crisp Cookie Cups

Peel apples, then dice into small bite-sized pieces about a quarter inch. Place apple pieces in a large mixing bowl. Add cinnamon, nutmeg, corn starch, brown sugar and white sugar to the apples. Toss well to coat the apples evenly.

Place a large skillet over medium-high heat. (I’ve used cast iron here but any skillet works.) Melt the butter, then add the apple mixture. Cook apples for 2-3 minutes or until they just begin to soften.

Chopped apples covered in cinnamon and sugar starting to cook in butter in a pan for the filling of apple cookie cups.

Diced cooked cinnamon apples being stirred for the filling of apple cookie cups.

Pour water into apple mixture. Continue to cook apples over medium heat for about 10 minutes, stirring frequently. The apples will begin to caramelize and the liquid will begin to thicken. Then remove apples from the heat and set to the side.
Preheat the oven to 350. Butter a muffin pan, or spray well with non-stick cooking spray or baking spray.
Scoop dough in 1 1/2 tablespoon scoops and place the dough into the bottom of a muffin tin with regular-size muffin cups. I find the easiest way to portion quickly and evenly is to use a medium cookie scoop.

Portions of cookie dough being placed in a greased muffin tin for apple cookie cups, with a scoop and cookie dough packaging on a cutting board nearby.

Close up a muffin pan with sugar cookie dough pressed into the bottom of one cup for apple cookies cups.

Press the dough in the bottom of each muffin tin. Mold the dough up the sides of the muffin tin about ¾ of the way to the top. You can also use the bottom of a small shot glass to press into the dough and shape the dough. The dough layer will feel thin, but don’t worry it will thicken as it bakes.
Place the muffin pan in the oven. Bake for 11-12 minutes or until the edges of the dough just start to turn a light golden brown. Allow the cookie cups to cool in the pan for about 10 minutes. Gently with the edge of a spatula or butter knife, gently remove the cookie cups to cool completely on a wire rack.

A skillet of cooked cinnamon apples next to a cooling rack with cookie cup shells for apple cookie cups.

Two mini filled apple cookie cups on a wire rack next to more cookie shells.

Once cool, scoop the apple mixture into the center of each cookie cup to fill. Then enjoy cold, or can also be served warm.

Wide view of apple cookie cups served on a cutting board.

Need more cozy baking ideas? Try the apple cider donut cake when feeding a bigger crowd. My apple cider donut holes are the perfect poppable size for kids. Or try my two ingredient pumpkin muffins or two ingredient pumpkin brownies for more easy but cozy ideas!

Variation Ideas

Drizzle with Caramel – Use store-bought or homemade caramel for an extra gooey, bakery-style bite.
Top with Whipped Cream – A swirl or dollop makes these feel just like mini pies, especially served warm.
Serve with Ice Cream – Pair with vanilla or butter pecan for a cozy fall dessert plate, or cinnamon ice cream if you can find it!
Add a Crumble Topping – Sprinkle the crumble from my apple crisp pizza on top before baking for more crunch.
Sprinkle with Nuts – Chopped pecans or walnuts add a nice crunch. These also make a great holiday treat on a platter next to my mini pecan chocolate pies.
Switch the Spices – Try pumpkin pie spice or apple pie spice instead of cinnamon and nutmeg for a twist.

What Apples Can I Use?

For the best apple crisp cookie cups, choose apples that hold their shape when baked. Granny Smith is my top choice, but Honeycrisp, Pink Lady, Fuji, and Cortland all work well. A mix of tart and sweet apples gives the most flavor.

Tart Apples (great for balancing sweetness in treats)

Granny Smith – Tangy, firm, and my go-to for baking.
Pink Lady – Crisp with a tart-sweet flavor.
Cortland – Mildly tart and softens just enough in baking.

Sweet Apples (milder flavor, softer texture)

Honeycrisp – Juicy, crisp, and sweet.
Fuji – Firm, sweet, and widely available.
Golden Delicious – Softens more, so pair with a tart apple for balance.

Other apples can fall into these categories too, grocery store signs often tell you if an apple is good for baking. Avoid Red Delicious as they turn mushy and lose flavor. Store apples in the fridge to keep them fresh longer, especially if prepping ahead for the holidays.

FAQ About Apple Cookie Cups

Can I use homemade sugar cookie dough?

Yes! Just make a half batch of my homemade sugar cookie dough so the dough isn’t too thick in the muffin cups.

Can I swap canned apple pie filling for fresh apples?

Yes, just dice the apples in the filling smaller and drain excess syrup so the cups don’t get soggy.

How do I keep the cookie cups from sticking?

Grease the muffin tin really well, or use a silicone muffin pan for easy removal.

Do these need to be refrigerated?

Yes, store in an airtight container in the fridge for up to 3 days.

Can I make them ahead of time?

Yes! Store cookie cups and filling separately, then fill before serving so they stay crisp.

Can I freeze them?

Yes, freeze the cookie cups and apple filling separately. Thaw the cookies, warm the filling in a pan, then assemble before serving.

What’s the best apple to use?

I like Granny Smith for a tart bite, but Honeycrisp, Pink Lady, or Fuji are also great choices.

How Long Do These Apple Crisp Cookie Cups Last?

Store cookie cups in the refrigerator in an airtight container for up to three days for best freshness. These cookie cups do taste best when fresh, and even better served warm.