These gluten free Coconut Chocolate Chip Cupcakes are super flavorful! They're made with coconut milk, chocolate ganache, and toasted coconut.
If you're looking for a fun and festive dessert, be sure to check out these Chocolate Chip Coconut Cupcakes. You'd be hard pressed to find a better flavor combination than chocolate and coconut!

Cupcakes are one of those things that makes every occasion feel a little more fun and festive. They're great for parties during the holiday season because they're basically individually sized desserts that are easy to transport.
These cupcakes are moist and flavorful. If you love coconut and chocolate, this is the dessert for you. The batter is made with coconut milk, coconut extract and the cupcakes are topped with a coconut ganache and toasted coconut.
The cupcakes are moist and packed with mini chocolate chips, giving them kind of a whimsical feel. They're dipped with chocolate ganache and then topped with toasted coconut. I love these cupcakes because they're not overly sweet, but just sweet enough to keep you coming back for more.
They're great for celebrating just about any holiday throughout the year. These cupcakes are a great choice for Christmas or New Year's Eve or a summer picnic or BBQ.
Jump to:
- Which Flour Is Best For Gluten Free Cupcakes?
- Which Coconut Milk Is Best For Baking?
- Ingredients For Coconut Chocolate Chip Cupcakes
- How To Make Coconut Chocolate Chip Cupcakes
- Which Chocolate Chips Are Best For Baking?
- How Long Do Chocolate Chip Cupcakes Take To Bake?
- How To Make Toasted Coconut
- How To Make Chocolate Ganache
- Top The Coconut Chocolate Cupcakes
- What To Serve With Coconut Chocolate Cupcakes
- How Long Do These Cupcakes Last?
- Can They Be Frozen?
- Coconut Chocolate Chip Cupcakes

Which Flour Is Best For Gluten Free Cupcakes?
This recipe is gluten free and calls for a gluten free flour blend. My go-to gluten free flour blend when making things like cupcakes, muffins, waffles, pancakes or any other baked good is Bob's Red Mill 1 to 1 Flour.
Bob's Red Mill 1 to 1 Flour is a gluten free flour blend that works much the same as a traditional all-purpose flour. It's made with a blend of gluten free flours, starches, and xanthan gum, which means that there is no need to add or sub any ingredients.
Other great gluten free flour blends include Cup4Cup or King Arthur Measure for Measure.
No matter which brand you choose, it's important that you use a gluten free flour blend, which contains the necessary starches and xanthan gum and not a gluten free all-purpose flour, which requires the addition of starches and gums.
You can find any number of quality gluten free flour blends at any grocery store or superstore these days, or it can be purchased online.
Feel free to use AP flour to make these Coconut Chocolate Chip Cupcakes if gluten is not an issue for you.

Which Coconut Milk Is Best For Baking?
Coconut milk is added to the batter as well as the chocolate ganache topping of these cupcakes. It's a great ingredient to use in baking because of its natural coconut flavor and high fat content.
It helps to make these cupcakes moist and gives the chocolate ganache topping a nice texture and sheen.
When it comes to baking, I recommend using a can of unsweetened, full fat coconut milk. Make sure to choose a quality brand that's gluten free (if gluten is an issue for you) without any added added ingredients like gums or emulsifiers if possible.
It's also important that the coconut milk is unsweetened, or these cupcakes will be too sweet.
Coconut milk may be found in the Asian or ethnic foods aisle of your local grocery store or purchased online.
Make sure to choose canned coconut milk and not the coconut milk from a carton or box or coconut cream.
Ingredients For Coconut Chocolate Chip Cupcakes
Here's what you'll need to make them.
- 1 ½ cups Gluten Free Flour Blend (or AP flour if not gluten free)
- 1 tsp. Baking Powder
- ½ tsp. Baking Soda
- ¼ tsp. Kosher Salt
- ½ cup Unsalted Butter (softened, equals 1 stick)
- ¾ cup Granulated Sugar
- 2 large Eggs
- 1 ½ cups Coconut Milk (full fat, unsweetened) (split)
- 1 tsp. Coconut Extract
- 1 cup Semi-Sweet Mini Chocolate Chips
- 1 cup Unsweetened Coconut Flakes (also known as shredded coconut)
- 1 cup Semi-Sweet Chocolate Chips




How To Make Coconut Chocolate Chip Cupcakes
These Coconut Chocolate Chip Cupcakes are easy to make and don't require any complicated ingredients or instructions.
The first step is to prepare the batter and then to add the mini chocolate chips. The batter is scooped into a lined muffin tin and the cupcakes are baked until light and fluffy.
The cupcakes are then cooled and dipped into a homemade coconut chocolate ganache. They are then topped with toasted coconut for extra flavor and texture.
- Preheat the oven to 350 degrees Fahrenheit.
- Line a 12-cup muffin tin with cupcake liners.
- In a large mixing bowl, combine 1 ½ cups gluten free flour blend (or AP flour if not gluten free), 1 tsp. baking powder, ½ tsp. baking soda, and ¼ tsp. of kosher salt. Mix together with a fork until completely combined.
- Using the whisk attachment of a stand mixer or a hand mixer, beat ½ cup (equals 1 stick) of softened, but not melted butter and ¾ cup of granulated sugar. Beat the butter and sugar for 3 minutes or until light and fluffy.
- Add 2 large eggs to the butter and sugar mixture, one at a time. Add one egg and beat for 30 seconds and then repeat (the butter mixture will look slightly chunky at this point).
- In a third bowl, combine 1 cup (using a dry measuring cup) of unsweetened coconut milk and 1 tsp. coconut extract. Stir the coconut milk mixture until it is soft and creamy.
- The next step is to combine all of these ingredients into one bowl. This process is done in stages to ensure that all of the ingredients get mixed together correctly.
- Add half of the flour mixture to the butter mixture and stir. Then add half of the coconut mixture and stir.
- Repeat with the rest of the flour and remaining coconut milk. The batter should be thick and slightly dense.


Which Chocolate Chips Are Best For Baking?
When it comes to adding chocolate chips to things like cupcakes, muffins, or pancakes, I love semi-sweet mini chocolate chips.
Mini chocolate chips remain intact during the baking process, which means that the chocolate doesn't melt and completely overtake the flavor of these cupcakes.
They distribute evenly throughout the batter and don't sink to the bottom of the cupcakes.
Semi-sweet mini chocolate chips are not overly sweet and provide nice little pops of chocolate flavor throughout the cupcakes.
- Once the batter is combined, add 1 cup of semi-sweet mini chocolate chips to the bowl.
- Stir the chocolate chips into the batter until completely combined.


How Long Do Chocolate Chip Cupcakes Take To Bake?
It takes about 20-22 minutes to bake these chocolate chip cupcakes at 350 degrees Fahrenheit.
Baking times may vary slightly, depending on the oven and type of muffin tin used.
The muffins should become slightly golden as they bake and are done when a toothpick inserted into the center comes out clean.
- Using an ice cream scoop, divide the batter evenly into the 12 muffin cups (this helps to ensure that there is an equal amount of batter in each muffin cup). There should be enough batter to fill all 12 cups nearly to the top.
- Place the muffin in the oven and bake for 20-22 minutes at 350 degrees Fahrenheit.
- The cupcakes should be lightly golden on top and spring back to the touch. A toothpick inserted into the center should come out clean when the cupcakes are finished baking.
- Remove the muffin tin from oven when finished and allow the cupcakes to cool completely before adding the toppings.

How To Make Toasted Coconut
Toasted coconut adds great texture to these cupcakes in addition to boosting the coconut flavor.
The process of toasting coconut is easy and can be done after the cupcakes have finished baking and are in the process of cooling. It only takes 6-10 minutes to toast the coconut.
Toasting the coconut helps to bring out its natural flavor and sweetness as well as creating a crunchy texture.
- Add 1 cup of unsweetened coconut flakes (also known as shredded coconut) to a pie plate, small cake pan, or baking sheet and spread evenly across the surface.
- Place the pan into the oven and toast the coconut for 6-8 minutes at 350 degrees Fahrenheit.
- Remove the pan and shake the coconut every 2 minutes to prevent the coconut from burning.
- Continue for 6-8 minutes, or until the coconut flakes are slightly golden brown.
- Remove the pan from the oven and set aside to cool.
It's important to keep a close eye on the coconut as it toasts so that the sugars in the coconut flakes don't burn, but instead turn golden brown.

How To Make Chocolate Ganache
These cupcakes are topped with a chocolate ganache as opposed to a traditional frosting. I love chocolate ganache because it has a rich, deep flavor and is not overly sweet. I use it as a topping for cookies, cakes, and even doughnuts.
Chocolate ganache is made using only two ingredients; chocolate and heavy cream. This version is made with coconut milk in place of heavy cream, which helps to amplify the coconut flavor of the cupcakes.
This recipe calls for semi-sweet chocolate chips and full fat coconut milk, which are combined and melted over a double boiler. I recommend regular semi-sweet chocolate chips and not mini chocolate chips, as the mini chocolate chips contain stabilizers and do not melt as well, which can result in a grainy ganache.
- To make the ganache, place a few cups of water into a double boiler and bring to a low boil.
- Place 1 cup of semi-sweet chocolate chips into the top portion of the double boiler.
- Once the chocolate chips begin to melt, add ½ cup of full fat, unsweetened coconut milk (using a dry measuring cup) to the chocolate chips.
- Allow the chocolate and coconut milk to melt and stir with a small whisk until the mixture is smooth and creamy (it will be slightly chunky at first).
- Pour the ganache into a small bowl when it's finished.


Top The Coconut Chocolate Cupcakes
Once the cupcakes are cooled, the coconut toasted, and the ganache prepared, it's time to add the toppings.
It's important that the cupcakes are cooled so that the ganache sticks to them. Keep in mind that the ganache does not completely harden, but should remain intact after dipping the cupcakes.
- To top the cupcakes, simply dip each one into the bowl of chocolate ganache and swirl until completely covered in the ganache.
- Repeat with the remainder of the cupcakes.
- Sprinkle a generous amount of the toasted coconut onto the ganache, making sure that it sticks to the surface.
You will likely have extra ganache after dipping all of the cupcakes. Chocolate ganache is a great thing to have on hand and can be used to make all types of desserts!
Here are some ways to use extra chocolate ganache:
- As chocolate syrup drizzled over ice cream
- Used to make chocolate truffles
- Used to make frosting
- As a glaze for cookies, doughnuts, or bars
- As a dip for fruit
Leftover chocolate ganache may be stored in an airtight container in the refrigerator for up to a week.

What To Serve With Coconut Chocolate Cupcakes
Cupcakes are perfect for parties and make a great dessert for any get-together. They pair nicely with all types of party desserts.
I love cupcakes with a cup of coffee or some espresso, but you can serve them with your favorite beverage. For an extra decadent treat, serve them with this Baileys Affogato Coffee Cocktail.
They're also delicious paired with an espresso martini or cocktails like a Raspberry Mule, Pomegranate Mojito, or Tom and Jerry Cocktail.
For a nonalcoholic pairing, check out this Cranberry Ginger Beer Mocktail.

How Long Do These Cupcakes Last?
These cupcakes should last 2-3 days stored in an airtight container at room temperature or in the refrigerator. Be sure to allow the cupcakes to cool completely before transferring to the fridge for storage.
Can They Be Frozen?
I do not recommend freezing these cupcakes, as they would likely dry out in the freezer.
Love chocolate? Check out these recipes!
- Italian Chocolate Hazelnut Cake
- Peppermint Chocolate Cheesecake Cups
- Halloween Puppy Chow
- Halloween Chocolate Cookies
- Cookies and Cream Ice Cream
Looking For More Coconut Desserts? Don't Miss These!
Toasted Coconut Marshmallows
Coconut Cream Pie
Coconut Flour Cake
Chocolate Dipped Coconut Macaroons

Coconut Chocolate Chip Cupcakes
Equipment
Ingredients
For The Cupcakes:
- 1 ½ cups gluten free flour blend or AP flour if not gluten free
- 1 tsp. baking powder
- ½ tsp. baking soda
- ¼ tsp. kosher salt
- ½ cup unsalted butter softened, equals 1 stick
- ¾ cup granulated sugar
- 2 large eggs
- 1 cup coconut milk full fat, unsweetened
- 1 tsp. coconut extract
- 1 cup semi-sweet mini chocolate chips
- 1 cup coconut flakes unsweetened, also known as shredded coconut
For The Chocolate Ganache:
- 1 cup semi-sweet chocolate chips
- ½ cup coconut milk unsweetened
Instructions
For The Cupcakes:
- Heat oven to 350 degrees Fahrenheit.
- Line a 12-cup muffin tin with cupcake liners.
- In a large mixing bowl, combine 1 ½ cups gluten free flour blend (or AP flour if not gluten free), 1 tsp. baking powder, ½ tsp. baking soda, and ¼ tsp. of kosher salt. Mix together with a fork until completely combined.
- Using the whisk attachment of a stand mixer or a hand mixer, beat ½ cup (equals 1 stick) of softened, but not melted butter and ¾ cup of granulated sugar. Beat the butter and sugar for 3 minutes or until light and fluffy.
- Add 2 large eggs to the butter and sugar mixture, one at a time. Add one egg and beat for 30 seconds and then repeat (the butter mixture will look slightly chunky at this point).
- In a third bowl, combine 1 cup (using a dry measuring cup) of full fat unsweetened coconut milk and 1 tsp. coconut extract. Stir the coconut milk mixture until it is soft and creamy.
- The next step is to combine all of these ingredients into one bowl. This process is done in stages to ensure that all of the ingredients get mixed together correctly.
- Add half of the flour mixture to the butter mixture and stir. Then add half of the coconut mixture and stir.Repeat with the rest of the flour and remaining coconut milk. The batter should be thick and slightly dense.
- Place the muffin tin in the oven and bake for 20-22 minutes. Rotate the pan halfway through the cooking process to ensure that all the cupcakes bake evenly. The cupcakes should be slightly golden on top when finished and spring back to the touch. You can also check them with a toothpick. Remove from oven and allow to cool completely.
- Once the batter is combined, add 1 cup of semi-sweet mini chocolate chips to the bowl.Stir the chocolate chips into the batter until completely combined.
- Using an ice cream scoop, divide the batter evenly into the 12 muffin cups (this helps to ensure that there is an equal amount of batter in each muffin cup). There should be enough batter to fill all 12 cups nearly to the top.
- Place the muffin in the oven and bake for 20-22 minutes at 350 degrees Fahrenheit.The cupcakes should be lightly golden on top and spring back to the touch. A toothpick inserted into the center should come out clean when the cupcakes are finished baking.
- Remove the muffin tin from oven when finished and allow the cupcakes to cool completely before adding the toppings.
For The Toasted Coconut:
- Add 1 cup of unsweetened coconut flakes (also known as shredded coconut) to a pie plate, small cake pan, or baking sheet and spread evenly across the surface.
- Place the pan into the oven and toast the coconut for 6-8 minutes at 350 degrees Fahrenheit.Remove the pan and shake the coconut every 2 minutes to prevent the coconut from burning.
- Continue for 6-8 minutes, or until the coconut flakes are slightly golden brown.Remove the pan from the oven and set aside to cool.
For The Chocolate Ganache:
- To make the ganache, place a few cups of water into a double boiler and bring to a low boil.
- Place 1 cup of semi-sweet chocolate chips into the top portion of the double boiler.Once the chocolate chips begin to melt, add ½ cup of full fat, unsweetened coconut milk (using a dry measuring cup) to the chocolate chips.
- Allow the chocolate and coconut milk to melt and stir with a small whisk until the mixture is smooth and creamy (it will be slightly chunky at first).Pour the ganache into a small bowl when it's finished.
- To top the cupcakes, simply dip each one into the bowl of chocolate ganache and swirl until completely covered in the ganache. Repeat with the remainder of the cupcakes.Sprinkle a generous amount of the toasted coconut onto the ganache, making sure that it sticks to the surface.






Theresa
These look so good! I wish my daughter liked coconut. I will just make half the batch with coconut, and half without.
Christine
That would definitely work and they should be just as tasty!
Jenni LeBaron
Yes, please! These look awesome. I love all of the many ways to include extra coconut in these!
Christine
You can never have too much coconut, right? 🙂
Liz
Coconut and chocolate are one of my favorite pairings! Such yummy cupcakes!
Christine
Thanks, Liz!
Claire
Coconut and chocolate is just the best combination!
I love the chocolate ganache topping as well as chips in the cupcakes!!! Double chocolate YUM!!!!
Christine
You can never have too much chocolate, right?!
Ana Hernández
I’ve made this recipe twice, and the only word I have to describe it is PERFECTION!!
It’s got a perfect balance between the sweetness, the puffiness and the humidity of the bread, these cupcakes are heaven on earth!!????????????
Christine
Hi Ana - Thank you so much for the feedback and I'm so glad you enjoyed them! 🙂
Nina
Would vanilla extract work in a pinch if coconut extract isn’t available?
Christine
Hi Nina - Absolutely! That should be no problem at all. 🙂
Hannah
If I don't want to use chocolate chips should I double the amount of coconut?
Christine
Hi Hannah - I think there should be enough coconut flavor in these cupcakes as the recipe uses coconut milk, coconut extract, and coconut flakes. You could probably add some coconut flakes to the batter if you like but it probably isn't necessary. I'd love to hear if you give them a try! 🙂
Camilla Hawkins
What a fab flavour combination, my family will be all over these cupcakes! Thank you for sharing my cookies:-)