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Chocolate Chip Cookie Cups with Ganache Filling

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5 from 4 votes
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Chocolate Chip Cookie Cups with Ganache Filling are a fun variation on a classic cookie. Simply bake low carb chocolate chip cookie dough in a muffin tin, make a well, and fill with rich chocolate ganache for a decadent keto treat.

close up of chocolate chip cookie cup stack with top cup sliced in halfPin

I’ve been working on a chocolate chip cookie recipe for the last few years off and on. My most recent attempt was delicious but the cookies fell apart. I decided to try the same dough in chocolate chip cookie cups and it worked perfectly!

Add a little chocolate ganache filling and you have a unique treat to satisfy your chocolate craving in about half an hour.

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How to make Chocolate Chip Cookie Cups

If you’ve ever made cookies you can make these.

  1. Mix the dough in a food processor or electric mixer.
  2. Fold in the chocolate chips.
  3. Divide the dough between sprayed, lined muffin tins.
  4. Bake.
  5. Make wells in the baked and cooled cookies.
  6. Pour in the ganache.

Unofficial step 8: try not to eat more than 2 or 3.

ingredients for chocolate ganache in measuring cup from above

How to Make Ganache Filling

Stir together hot cream, sweetener, and chocolate chips for the ganache filling.

I prefer at this point to pour the ganache into a small food processor or blender and blend for a minute or two. This helps it thicken and makes it unbelievably smooth. Much more than you can get just by stirring.

measuring cup and whisk full of chocolate ganache filling

What type of chocolate should I use?

I use sugar-free semisweet chocolate chips in this recipe. I buy Lily’s when I can get it on sale but I’ve also made my own chocolate chips before. It’s a little labor intensive though and I’m not really sure the time commitment is worth the small savings.

If you’d like to make your own chocolate chips just melt unsweetened chocolate, add a little refined coconut oil, and sweetener to taste and pour into a chocolate chip mold or some silicone thing with small shapes. I use my pyramid baking mat upside down. I know some other people who use silicone trivets.

muffin tin fill of small chocolate chip cookies before being shaped into cups

What other fillings can I use in these Chocolate Chip Cookie Cups

Just about anything you can dream up! On my to try list are:

Peanut Butter Frosting

Vanilla Ice Cream

Hot Fudge

Salted Caramel

and last but not least…

No-Bake Chocolate Cheesecake Filling!

wooden dowel used to shape cookie cups placed on muffin tin of shaped cookie cups

Do I need a tart tamper for Cookie Cups

You don’t. You can use any kitchen tool, gadget, or just your thumbs to make the wells in the cookie cups. You want about 1/3 inch border around the edges.

I do love my tart tamper and use it at least every couple of months. But I’m a bit of a kitchen gadget hoarder and kitchen gadgets are one of my love languages. I’ll admit it.

measuring cup of chocolate ganache filling being poured into chocolate chip cookie cups in a muffin tin

How to store Cookie Cups?

I store these in the fridge if we are going to keep them for more than a few days (i.e. hide them from my family and not share). But the ganache filling will firm up a little more like fudge with extended time in the fridge.

stack of chocolate chip cookie cups with one cup cut in half, one half tops the stack while the other half leans on the stackPin

 

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close up of ganache filling in sliced chocolate chip cookie cup

Chocolate Chip Cookie Cups with Ganache Filling

Taryn Scarfone
Chocolate Chip Cookie Cups with Ganache Filling are a fun variation on a classic cookie. Simply bake low carb chocolate chip cookie dough in a muffin tin, make a well, and fill with rich chocolate ganache for a decadent keto treat.
5 from 4 votes
Prep Time 15 minutes
Cook Time 15 minutes
Total Time 30 minutes
Course Dessert
Cuisine American
Servings 12
Calories 260

Ingredients
 
 

Cookie Dough:

Ganache Filling

Instructions
 

  • Preheat the oven to 350. Put aluminum cupcake liners into 12 holes of a regular muffin tin. Spray with cooking spray.
  • Put the first 3 ingredients into a food processor. Pulse until the dough starts to come together.  Put all the remaining cookie ingredients (except the chocolate chips) into the food processor and process until a ball of dough forms. Scraping down the sides as needed. Fold in the chocolate chips.
  • Divide batter between the holes of the prepared tin. Bake for 13-15 minutes or until golden brown. Cool for 5 minutes. Press with a tart tamper to make a well.
  • Make the ganache by heating the cream in the microwave or in a small pan until bubbles form around the edge. Do not boil. This takes about 1 minute in the microwave. Add the chocolate and sweetener and stir until smooth. Blend with a stick blender for an extra smooth ganache. Fill the cooled cookie cups with the ganache.

Notes

*** I get a lot of comments from my low carb readers on the use of molasses. I use it for flavor, not sweetness. One teaspoon of molasses has 5 grams of carbs. This recipe uses 1 tsp divided by 12 servings. That is less than .5 grams of carbs from the molasses per cookie. If you prefer you can just omit it.    
Notes on Sweeteners: 
I use my own blend of xylitol, erythritol, and stevia in my recipes. This is twice as sweet as sugar. It is comparable to Trim Healthy Mama Gentle Sweet and Truvia.
To sub in Swerve or Lakanto Monk Fruit use 1.5 times the amount of sweetener called for. 
 
To sub in Pyure or Trim Healthy Mama Super Sweet use half the amount of sweetener called for.
 
Substitutions will work in most recipes. They may not work in candies, such as caramel.

Nutrition

Serving: 1cookie cupCalories: 260Carbohydrates: 7gProtein: 5gFat: 26gSaturated Fat: 13gCholesterol: 52mgSodium: 208mgPotassium: 163mgFiber: 3gSugar: 1gVitamin A: 460IUCalcium: 52mgIron: 3.4mg
Love this recipe?Please leave a 5 star rating!

 

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16 Comments

    1. Yes, I’ve frozen them successfully. Depending on how long they are in the freezer the chocolate ganache might get a bit of a ‘bloom’ (when chocolate gets a white coating) but that wouldn’t affect the taste.

  1. My cookie dough after baking for 15 minutes is liquid in the middle. I used ⅔ c. Plus 2Tbsp. and 2 tsp. of monk fruit. I popped the butter in the freezer to cool it before I made the dough. Did I do something wrong, or do I just need more flour?

  2. Just when I thought chocolate chip cookies couldn’t get any better!! Haha the chocolate ganache takes things to the next level!5 stars

  3. Hi! I made these last night (just the cookie, but did not fill them with anything). The taste was great, but my cookies seem quite a bit greasier than yours seem to be in the pictures. I used 4 oz of butter, which came out to half a stick. Should I have used 4 T instead? Thank you!

      1. No, a stick of butter is correct. I do not like this dough just as cookies, but it works well for cookie cups.

5 from 4 votes (1 rating without comment)

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