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    Home » Gluten Free Dessert Recipes » Gluten Free Cookie Recipes

    Chocolate Filled Cookies

    Published: Aug 2, 2025 by Lee · This post may contain affiliate links · 1 Comment .

    Jump to Recipe Jump to Video

    These Chocolate Filled Cookies are soft and chewy cookies, stuffed with chocolate and loaded with chocolate chips! No mixer is used to make these and with only 30 minutes of chilling, these cookies could not be more simple to make! Best yet, they're gluten free, nut free, eggless and can easily be made vegan!

    Three halves of Chocolate Filled Cookies oozing delicious warm chocolate goodness.

    These Chocolate Filled Cookies take regular chocolate chip cookies to the next level! With only a few additional steps and zero additional ingredients, these stuffed chocolate chip cookies are so easy not make and are sure to be a hit with all your family and friends!

    For more chewy chocolate chip cookie recipes, try my Small Batch Chocolate Chip Cookies, my Eggless Chocolate Chip Cookies, my No Butter Chocolate Chip Cookies and my Dark Chocolate Chip Cookies!

    Jump to:
    • Reasons to Love These Stuffed Chocolate Chip Cookies
    • Ingredient Notes
    • Substitutions and Variations
    • How to Make Chocolate Filled Cookies
    • Expert Baking Tips
    • Recipe FAQs
    • More Cookies Recipes You'll Love
    • 📖 Recipe
    • Chocolate Filled Cookies

    Reasons to Love These Stuffed Chocolate Chip Cookies

    • Allergy Friendly- These cookies are gluten free, nut free, egg free and can easily be dairy free (vegan)!
    • Oozing with Chocolate- These cookies are gooey and soft in the middle and oozing with chocolate! 
    • Crispy Edges- The first day the cookies have soft and chewy middles with crispy edges. After storing them overnight, they become softer on the edges.
    • Chocolate Chips- The cookies are loaded and topped with chocolate chips! 
    • Easy to Make- You don't need a mixer of any kind to make these like my Frosted Chocolate Cookies! All you need is a whisk and a spatula to create this fast cookie recipe!

    Ingredient Notes

    Multipurpose gluten free flour, light brown sugar, butter, cornstarch water, chocolate chips, milk, baking soda, pure vanilla extract, and kosher salt in separate containers.
    • Gluten Free Flour- If you also have nut allergies, make sure to use a brand that’s made in a nut free facility.  I really love to use this gluten free flour because it’s free of the top 9 allergens. It also contains xanthan gum which really helps give baked goods their bounce and prevents them from falling apart.
    • Butter/ Vegan Baking Stick- For this recipe we are actually using melted butter. Make sure it's cooled prior to using.
    • Light Brown Sugar- I use light brown sugar instead of granulated for added moisture. I prefer light brown to dark brown in this recipe; too much additional moisture can cause the cookies to spread while baking.
    • Cornstarch and Water- These cookies have no egg so this mixture helps bind everything together. You need this otherwise the cookies will spread into a liquid mess while baking.
    • Milk- If there are no dairy allergies or if you’re not vegan, you can use regular whole milk. For non-dairy, use a dairy-free milk of your choosing. 
    • Vanilla- Make sure to only use pure vanilla extract otherwise the cookies can have a chemical flavor.
    • Chocolate Chips- To keep vegan, make sure to use gluten free/vegan chocolate chips. I love these allergy friendly chocolate chips.

    See my recipe card below for a complete list of the ingredients with measurements.

    Substitutions and Variations

    How to Make these into Vegan Chocolate Chip Cookies

    • Use a gluten free flour that’s free from dairy.
    • Make sure the brand of sugar you use is vegan. 
    • Use vegan baking sticks instead of butter.
    • Only use a non-dairy milk of choice.
    • Read the label on your chocolate chips to ensure they’re gluten free, nut free and vegan. 

    Make this Recipe with All Purpose Flour

    • Use 1 ¾ cups packed AP flour (294 grams).
    • Use 2 tablespoons milk.
    • You still need to chill the dough due to the lack of eggs.

    This recipe has not been tested with some of these substitutions and/or variations due to celiac disease and food allergies. If you change any of the ingredients, please let us know how the recipe turned out in the comments below!

    Pulling apart a chocolate filled cookie with gooey sugary chocolate connecting the halves.

    How to Make Chocolate Filled Cookies

    Here are the step by step instructions for making these stuffed chocolate chip cookies!

    Fully melted chocolate chips in a bowl.

    Step 1: Make the Filling

    Microwave the chocolate chips in a medium heat safe bowl in 10-15 second increments, stirring after each time, until the chocolate chips are fully melted.

    Dollops of chocolate on parchment paper.

    Step 2: Freeze the Filling

    Use a teaspoon to create 16 dollops of the liquid chocolate on a parchment lined small sheet pan and pop in the freezer.

    A pool of yellow melted butter.

    Step 3: Melt the Butter

    Microwave the butter in 11 second increments until partially melted. Whisk until fully melted; the residual heat will melt the rest. Set aside to cool.

    Do not microwave until it bubbles or browns.

    A whisk with the white dry ingredients.

    Step 4: Whisk Together the Dry Ingredients

    In a medium bowl, whisk together the gluten free flour, baking soda and kosher salt. Set aside.

    Milky white cornstarch water in a bowl.

    Step 5: Make the Cornstarch Water

    In a small bowl, using a spoon, mix together the cornstarch and water until thin and watery. It will be thick and tacky at first.

    Light brown sugar and vanilla mixed into the cornstarch water.

    Step 6: Mix in the Sugar, Cornstarch Water and Vanilla

    Into the cooled melted butter, whisk in the light brown sugar, the cornstarch water and the pure vanilla extract until fully combined.

    Mixing in hundreds of chocolate chips.

    Step 7: Add in the Flour Mixture, Milk and Mini Chocolate Chips

    Starting and ending with the flour mixture, whisk half the flour into the melted butter mixture. Add the milk and whisk until combined.

    Using a spatula, gently fold in the rest of the flour until combined. Do not over mix or the dough will become shiny and too sticky.

    Fold in the chocolate chips.

    Pressing the chocolate dollops into a scooped ball of cookie dough.

    Step 8: Chill and Form into Balls and Stuff

    The dough will be very sticky. Add it to a freezer safe bowl, cover the top with plastic wrap and freeze for 30 min.

    After 30 min, using a large cookie scoop, make 16 scoops with the dough.

    If the dough is sticking to the cookie scoop, wash the scoop half way through to get off any stuck on dough.

    Take one of the dough balls and press your thumb into the center to make a well. Shove one of the chocolate discs into the hole.

    A disc of cookie dough topped with extra chocolate chips.

    Step 9: Form into Discs and Add Additional Chocolate Chips

    Cover up the chocolate filling with the dough that’s been pressed to the side to reform into a thick disc.

    Next, press the tops of the dough discs into the extra chocolate chips. Gently press down on the chips so they stick to the dough.

    Fresh baked and warm Chocolate Filled Cookies.

    Step 10: Bake the Cookies and Cool

    Place the dough balls about 3-4 inches apart on the parchment lined baking sheet. Bake the cookies at 350 degrees Fahrenheit for 16 minutes.

    Immediately reshape the cookies when they come out of the oven and let cool on the baking sheet for 5 min before transferring to a cooling rack.

    Expert Baking Tips

    • Use Packed Cups of Flour- Normally in baking we do not use packed cups however, when working with gluten free, I've found using packed cups works best to help the baked goods keep their shape. For this recipe use packed cups or please read the gram amount.
    • Use Cooled Melted Butter- Make sure the butter is not bubbling or browned. Do not microwave it too much. Microwave the butter until there is a little bit left unmelted. Then whisk until the residual heat melts the rest of the butter. Then set it aside to cool as you prep the rest of the recipe. When it is time to use the butter it should be cool and thick/creamy. You can see in my video.
    • Freezing the Dough- If you don’t freeze the cookie dough for at least 30 minutes, the dough will be too sticky to form into scoops. 
    • Wash the Cookie Scoop- If you notice the dough getting stuck in the cookie scoop, wash and dry your cookie scoop halfway through making the dough balls.
    • Add the Flour then Milk then More Flour- Do not add the milk with the wet ingredients otherwise the batter will be too wet and shiny and the cookies will be very buttery and flakey. You must add half the flour, then the milk and then the rest of the flour.
    • Reshape the Cookies- For perfectly round cookies, reshape them as soon as they come out of the oven. Use a spatula to push them back into a circle shape.

    Recipe FAQs

    Can I make the dough of the stuffed cookies ahead of time?


    Yes. You can make the dough the day before. Keep it in a bowl and cover the top with plastic wrap in the fridge. 

    If doing this, there is no need to freeze the dough prior to baking.

    Can I make the cookies the day prior?


    Yes you can, but keep in mind the centers won't be gooey unless you microwave them.

    Can I use a different sugar other than light brown?


    Light brown sugar helps add moisture and gives the cookies their beautiful color since these are eggless.

    Do not use dark brown in this recipe; too much additional moisture can cause the cookies to spread too much while baking.

    How do I store these Chocolate Filled Cookies?


    Storing: Once the stuffed cookies have cooled, store them in an airtight container at room temperature for up to 3 days. 

    If you want the cookies warm and gooey, heat the cookie in the microwave for a few seconds prior to serving. Be very careful not to burn your mouth.

    Freezing Baked Cookies: To freeze already baked cookies, place cookies (not stacked) on a parchment lined baking sheet and pop in the freezer uncovered. Freeze for 10-15 minutes or until frozen. Once frozen, you can store them stacked in a freezer safe airtight container or zip top bag in the freezer for up to 1 month. To defrost, take the container out and leave at room temperature until soft. 1-2 hours. 

    A stack of halved Chocolate Filled Cookies reveals the warm cookie insides.

    More Cookies Recipes You'll Love

    • A bite through the sweet layers of ganache, frosting and cookie of the Strawberry Chocolate Cookie.
      Strawberry Chocolate Cookies
    • Pools of caramel ooze from the sweet Rolo shards atop the chocolate Rolo Cookies.
      Rolo Cookies
    • Chocolate Chocolate Chip Cookie Bars are overloaded with melted chocolate chips on a warm chocolate base.
      Chocolate Chocolate Chip Cookie Bars
    • A bite into the soft and chewy Banana Bread Cookie reveals the warm interior.
      Banana Bread Cookies

    Did you try this recipe? Please leave me a ⭐ review below!

    Don’t forget to tag me on Instagram @laneandgreyfare and follow along on Pinterest, Facebook and YouTube! Enjoy!!!

    📖 Recipe

    Three halves of Chocolate Filled Cookies oozing delicious warm chocolate goodness.

    Chocolate Filled Cookies

    Author: Lee
    These Chocolate Filled Cookies are soft and chewy cookies, stuffed with chocolate and loaded with chocolate chips! No mixer is used to make these and with only 30 minutes of chilling, these cookies could not be more simple to make! Best yet, they're gluten free, nut free, eggless and can easily be made vegan!
    5 from 1 vote
    Print Recipe Pin Recipe
    Prep Time 20 minutes mins
    Cook Time 16 minutes mins
    Freeze Time 30 minutes mins
    Total Time 1 hour hr 6 minutes mins
    Course Dessert
    Cuisine American
    Servings 14 large cookies
    Calories 373 kcal

    Ingredients
     
     

    For the Chocolate Chip Cookies

    • 1 ¾ cups multipurpose gluten free flour (I use a gluten free multipurpose flour with xanthan gum already in it)
    • 1 teaspoon baking soda
    • ½ teaspoon kosher salt
    • 2 rounded tablespoons cornstarch mixed with 3 tablespoons water
    • ½ cup unsalted butter or vegan baking stick, melted and cooled
    • 1 ¼ cups light brown sugar , packed
    • 1 teaspoon pure vanilla extract
    • ¼ cup milk
    • 1 ¾ cups semi-sweet chocolate chips

    For the Filling

    • ¾ cup semi-sweet chocolate chips , melted

    Instructions
     

    • Place ¾ cup chocolate chips in a heat safe bowl.
      Heat them in the microwave in 10-15 second increments, stirring after each time until the chocolate chips are fully melted.
    • Use a teaspoon to create 16 dollops of the liquid chocolate on a parchment lined small sheet pan and pop in the freezer.
    • Place the ½ cup unsalted butter or vegan baking stick in a heat safe bowl. Place a paper towel on top of the bowl so the butter doesn't splatter. Microwave in 11 second increments until just melted. Do not let it bubble or brown. Set aside to cool.
      Do not microwave it too much. Microwave it until there is just a little bit of butter left unmelted and then whisk it and the residual heat melts the rest of the butter.
    • In a medium bowl, whisk together the 1 ¾ cups gluten free flour, 1 teaspoon baking soda and ½ teaspoon kosher salt. Set aside.
    • In a small bowl, using a spoon, mix together the 2 rounded tablespoons of cornstarch and the 3 tablespoons of water until thin and watery. It will be thick and tacky at first.
    • Into the cooled melted butter, combine the 1 ¼ cups light brown sugar, the cornstarch water and the 1 teaspoon pure vanilla extract. Whisk until it is all fully emulsified and blended. It may appear slightly chunky. That's normal.
    • Starting and ending with the flour mixture, whisk half the flour into the melted butter mixture. Then add the ¼ cup milk and whisk to combine.
      Add in the second half of the flour gently with a spatula. Do not over mix or the dough will become shiny and too sticky.
    • Still using the spatula, scrape down the sides of the bowl and fold in 1 ¼ cups of chocolate chips. Gently fold until everything is just combined and you don't see any more flour. Again, make sure not to over mix.
    • The dough will be very sticky. Add it to a freezer safe bowl, cover the top with plastic wrap and pop the entire bowl of dough in the freezer for 30 min.
    • When the dough is almost done chilling, preheat your oven to 350 degrees Fahrenheit and line a baking sheet with parchment paper. Do not grease.
    • Take the dough out of the freezer. Using an ice cream scoop or large cookie scoop (I use a 2 ounce cookie scoop), scoop the dough out into 16 scoops.
      If the dough is sticking to the cookie scoop, wash the scoop half way through to get off any stuck on dough.
    • Take one of the dough balls and press your thumb into the center to make a well.
      Shove one of the frozen chocolates into the hole and then cover it up with the dough that’s been pressed to the side.
      The dough should be shaped like a thick disc.
    • Pour the additional ½ cup chocolate chips into a small bowl. Press the tops of the dough discs into the chocolate chips. With your hand, gently press down on the chips so they stick to the dough.
    • Place the dough discs about 3-4 inches apart on the parchment lined baking sheet. Bake the cookies at 350 degrees Fahrenheit for 16 minutes.
      I only bake 6-8 at a time. Pop the rest of the dough discs in the freezer while the first batch is baking.
    • Immediately reshape the cookies when they come out of the oven. Use a spatula to push them into a circle.

    Video

    Notes

    Vegan: Use a dairy-free gluten free flour, vegan sugar, vegan baking sticks, a non-dairy milk and vegan chocolate chips.
    All Purpose Flour: I cannot test this due to celiac disease, but use 1 ¾ cup packed cups of flour (294 grams) and 2 tablespoons of milk. Still chill the dough. 
    Storing: Keep extra cookies in an airtight container at room temperature for up to 3 days. Warm in microwave a few seconds before serving if you want them warm and gooey. Be careful not to burn your mouth.
    Freezing: To freeze already baked cookies, place cookies (not stacked) on a parchment lined baking sheet and pop in the freezer uncovered. Freeze for 10-15 minutes or until the cookies are completely frozen. Once frozen, you can store them stacked in a freezer safe airtight container or zip top bag in the freezer for up to 1 month. To defrost, take the container out and leave at room temperature until soft. Warm in microwave a few seconds before serving if you want them warm and gooey. Be careful not to burn your mouth.

    Nutrition

    Calories: 373kcalCarbohydrates: 47gProtein: 4gFat: 20gSaturated Fat: 11gPolyunsaturated Fat: 1gMonounsaturated Fat: 6gTrans Fat: 0.3gCholesterol: 20mgSodium: 173mgPotassium: 217mgFiber: 4gSugar: 32gVitamin A: 226IUCalcium: 54mgIron: 3mg
    Tried this recipe?Let us know how it was!

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    Reader Interactions

    Comments

    1. John

      August 02, 2025 at 9:42 pm

      5 stars
      These cookies were so easy to make!

      Reply
    5 from 1 vote

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    Lee, the beautiful founder of Lane and Grey Fare.

    Hi guys, I'm Lee! As a mother of two children with celiac disease and multiple food allergies, I wanted to share all that I’ve learned with others in a way that’s entertaining and helpful. All my food is 100 percent gluten free, nut free, seed free, egg free and most of my baked goods can easily be made dairy free (vegan).

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