Chocolate Chip Cookie Cups with Ganache Filling
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.

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.

How to make Chocolate Chip Cookie Cups
If you’ve ever made cookies you can make these.
- Mix the dough in a food processor or electric mixer.
- Fold in the chocolate chips.
- Divide the dough between sprayed, lined muffin tins.
- Bake.
- Make wells in the baked and cooled cookies.
- Pour in the ganache.
Unofficial step 8: try not to eat more than 2 or 3.

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.

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.

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:
and last but not least…
No-Bake Chocolate Cheesecake Filling!

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.

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.

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Chocolate Chip Cookie Cups with Ganache Filling
Ingredients
Cookie Dough:
- 4 oz salted butter cold, cut into pieces
- 1 cup almond flour
- 1/3 cup Joy Filled Eats Sweetener (or see alternatives in recipe notes)
- 1 egg
- 2 oz cream cheese softened
- 1 tsp molasses ***
- 1 tsp baking soda
- 1 tsp vanilla
- 2/3 cup sugar-free chocolate chips
Ganache Filling
- 4 oz sugar-free chocolate chips
- 4 oz heavy cream
- 1/3 cup powdered sweetener
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
Nutrition








My kid has a tree nut allergy. Which flour would you recommend using instead?
Sunflower seed flour can be used 1:1 in place of almond flour.
Can you put these in the freezer?
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.
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?
Just cook them a little longer. Since you are pressing down the center and filling them with ganache it’s ok if they are a little soft.
in the picture they look like mini cups, are they regular size?
They are regular size, not mini.
Thanks for a great recipe. They came out perfect!
Can I use THM baking blend instead of almond flour?
Yes, use a little less.
Just when I thought chocolate chip cookies couldn’t get any better!! Haha the chocolate ganache takes things to the next level!
I love this idea and so did the kids!! Will have to make again as they are already gone.
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!
Sorry, I meant a whole stick…should I have only used a half stick of butter?
No, a stick of butter is correct. I do not like this dough just as cookies, but it works well for cookie cups.