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    Home » Cookies

    Dark Chocolate Cookie Cups (Gluten Free, Paleo)

    Published: Jul 14, 2026 · by Katie

    Jump to Recipe·Print Recipe

    These dark chocolate cookie cups consist of a crunchy chocolate cookie that's filled with a rich chocolate fudge. The cookie cups are made with tigernut flour, sweetened with coconut sugar and baked in a mini muffin pan. These cookie cups are gluten free, paleo, vegan and free from top allergens.

    Top down view of chocolate cookie cups topped with flaked salt.

    I love a good cookie cup recipe! And these ones are special because they're double chocolate and allergy friendly (no gluten, dairy, eggs, nuts or soy).

    They're the perfect bite-sized treat to share with guests or stash in the freezer for later. I made them multiple times and loved using them as mix-ins for my Ninja Creami ice cream.

    These dark chocolate cookie cups consist of a crisp chocolate cookie that's filled with a rich chocolate fudge. The cookie cup dough is made in one bowl, scooped into a mini muffin tin, shaped into cups and then baked.

    You'll love how easy these are to make and even easier to eat!

    Why You'll Love these Chocolate Cookie Cups

    • allergy friendly - no gluten, eggs, dairy, soy or nuts
    • paleo and vegan - made with simple, wholesome ingredients you can feel good about
    • rich chocolate flavor - these cookie cups aren't overly sweet and they're perfect for any chocolate lover.
    • easy to make - while there are a few steps required, this recipe is easy to follow and doesn't involve any complicated steps
    Grabbing a chocolate cookie cup.

    Ingredients

    You can find the full recipe for these dark chocolate cookie cups in the recipe card below, but here's an overview of the ingredients you'll need:

    • tigernut flour - this is an excellent nut free paleo baking flour. I love using it in my allergy friendly recipes. If you want to learn more about tigernut flour, check out my tigernut flour guide.
    • tapioca starch - needed for texture purposes. The best swap is arrowroot starch.
    • cocoa powder - since these are chocolate cookie cups. I used an organic Dutch processed cocoa powder for this recipe.
    • coconut sugar - to sweeten the dough for the cookie cups. You can swap coconut sugar for any other granulated sugar/sweetener.
    • baking soda - for a slight rise to the cookie cups.
    • salt - enhances the flavors.
    • palm shortening - this is a great dairy free, paleo friendly alternative to butter. However, you should be able to swap the shortening with butter.
    • water - to add moisture to the batter.
    • vanilla extract - for flavor
    • dark chocolate chips - for the fudge filling
    • sunbutter - for the fudge filling. You can swap sunbutter with any other nut or seed butter.
    Ingredients needed to make dark chocolate cookie cups.

    How to Make Dark Chocolate Cookie Cups

    These allergy friendly cookie cups are easy to make and a fun spin on your average cookie. Here's how to make them:

    1. First, preheat your oven to 350 degrees F.
    Combined dry cookie cup ingredients in mixing bowl.
    1. Combine the dry cookie ingredients.
    Dough for cookie cups.
    1. Mix in the wet ingredients and knead the dough until well combined.
    Dough rolled into balls and placed in a mini muffin pan.
    1. Scoop the dough into balls and place them in a miniature muffin pan. I recommend a silicone muffin pan for easy removal.
    Chocolate cookie cup dough in mini muffin pan, ready to bake.
    1. Use your fingers to shape the dough into cups. Then place the cookies in the oven and bake at 350 degrees for 14-15 minutes.
    Using the end of a large cookie scoop to make indentations in the baked cookie cups.
    1. After baking, remove the cookie cups from the oven and use a small circular object to press down the center of each cup. I used the end of a large cookie scoop to do this.
    Adding the fudge filling to the cookie cups.
    1. Melt the dark chocolate for the filling, then mix in the sunbutter. Fill each cookie cup to the top with the fudge mixture.
    1. Keep the cookie cups in the mini muffin tin until they have full cooled. Place them in the fridge for at least an hour for the filling to set.
    Close up of cookie cup.

    Storage

    These dark chocolate cookie cups are best stored in an airtight container or baggie. You can keep them at room temperature for a few days, in the fridge up to two weeks, or the freezer up to 3 months.

    More Cookie Cup Recipes

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      Sunbutter Cookie Cups (Paleo, Vegan)
    • Healthy Coffee Cookie Cups (No Bake, Gluten Free)
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      Hazelnut Cookie Cups (No Bake, Paleo)
    • Healthy Twix Cookie Cups (Vegan, Paleo)
    Print
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    Top down view of chocolate cookie cups topped with flaked salt.

    Dark Chocolate Cookie Cups (Gluten Free, Paleo)

    5 Stars 4 Stars 3 Stars 2 Stars 1 Star 5 from 1 review
    • Author: Katie
    • Prep Time: 30
    • Cook Time: 14
    • Total Time: 44 minutes
    • Yield: 17 mini cookie cups 1x
    Print Recipe
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    Description

    Crunchy dark chocolate cookies shaped like a mini cup and filled with a fudgy dark chocolate.


    Ingredients

    Scale

    Cookie Cups

    • 1 cup tigernut flour (90g)
    • ½ cup tapioca starch (62g)
    • ¼ cup cocoa powder (24g)
    • ¼ cup coconut sugar
    • ¼ tsp baking soda
    • ¼ tsp salt
    • ½ cup palm shortening (93g) room temperature
    • 2 Tbsp water
    • 1 tsp vanilla extract

    Filling

    • ⅓ cup dark chocolate chips
    • ⅓ cup sunbutter


    Instructions

    1. Preheat your oven to 350 degrees F.  Place a miniature silicone muffin pan on a metal baking sheet.
    2. In a large mixing bowl, combine the dry cookie cup ingredients.  This includes the tigernut flour, tapioca starch, cocoa powder, coconut sugar, baking soda and salt.
    3. Mix in the wet ingredients: shortening, water and vanilla.  Combine first with a fork or spatula, then use your hands to knead the dough until it is well combined.
    4. Using a small cookie scoop, scoop the dough and roll it into balls.  (Each ball of dough should be about 1 Tbsp.) Place the balls of dough in the miniature silicone muffin pan.
    5. Use your fingers to shape the dough into cups.
    6. Place the cookies in the oven and bake at 350 degrees for 14-15 minutes.
    7. After baking, remove the cookie cups from the oven and use a small circular object to press down the center of each cup. I used the end of a large cookie scoop to do this.  Keep the cookie cups in the mini muffin pan.
    8. Melt the dark chocolate for the filling, then mix in the sunbutter.
    9. Fill each cookie cup to the top with the fudge mixture.
    10. Place them in the fridge for at least an hour for the filling to set.

    Did you make this recipe?

    Share a photo and tag me — I can't wait to see what you've made!

    Pinterest image for dark chocolate cookie cups.
    « Mint Chocolate Tart (Paleo, Vegan, No-Bake)

    Reader Interactions

    Comments

    1. Katie

      July 14, 2026 at 11:53 am

      Hope you all love these cookie cups as much as we do!

      Reply

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    Hi there!

    I'm Katie and I have a passion for baking healthy treats using real, whole food ingredients. On my blog you'll find a variety of sweet and savory recipes, all gluten free and dairy free. My mission is to make baking nutritious, delicious, simple and family friendly.

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