Fudgy Coconut Flour Chocolate Cupcakes

These coconut flour cupcakes are loaded with rich cocoa flavor, and they're unbelievably moist and tender. Easy to make in one bowl in about 30 minutes. Allergy-friendly and free of dairy, gluten, grains, nuts, and refined sugar – though your guests will never know!

Top them with a double or triple batch of coconut milk chocolate ganache for an extra-chocolatey treat.

This coconut flour chocolate cake has become a community favorite recipe since I shared it in 2022. A few readers have asked if it could be made into cupcakes. It can! The recipe just needed a small tweak: a touch more coconut flour to prevent the cupcakes from sinking in the middles.

Coconut flour is the trickiest of the gluten-free flours to work with. This thirsty, fibrous flour soaks up moisture like nobody's business. But get the ratios just right and coconut flour will turn out a floofy, springy, and (in the case of these cupcakes) fudgy cake that no one will guess is gluten-free.

These paleo chocolate cupcakes are allergy-friendly and free of dairy, nuts, refined sugar, gluten, and grains. Whip up a batch for the chocophile in your life!

There's a lot to love about these coconut flour cupcakes. They're:

• Fudgy and tender
• super chocolatey
• moist for days
• easy to whip up with a bowl and whisk
• made in 30 minutes
• topped with luscious vegan chocolate ganache
• allergy-friendly (paleo, dairy-free, and nut-free)

Here's what one happy baker had to say about them:

Ingredients & Substitution Suggestions

Flours

This coconut flour cupcake recipe uses just one flour and one starch, both of which are easily found at most well-stocked grocers. See my guide to baking with gluten-free flours for more details!

• Coconut flour creates an airy and tender base. Coconut flour soaks up a lot of moisture, so only a small amount is needed here. I use Bob's Red Mill coconut flour, which is finely milled in a gluten-free facility from organic, fair trade-certified coconuts.
  • Coconut flour is tricky to substitute, so I recommend sticking with it in this recipe.
• Tapioca flour (aka tapioca starch) helps the cupcakes hold together thanks to its sticky power. It helps the cupcakes bake up with a fine and fluffy crumb that still has some chew just like gluten-based chocolate cupcakes.
  • Arrowroot can often stand in for tapioca flour, though I haven't tested it here.

Other Ingredients

• Cocoa powder acts like another flour here while adding rich chocolate notes. I use Dutch-process cocoa which is treated with alkali to make it less acidic. It has the mellow, classic flavor of a boxed cake mix. If you only have regular cocoa powder, it *might* work, but I haven't tested it this way.
• Vanilla Extract adds lovely floral flavor that enhances and deepens the chocolate taste. Be sure to use gluten-free vanilla extract if need be.
• Coconut milk moistens and enriches the batter. Be sure to use full-fat coconut milk that has been well-combined. If it's cold in your kitchen and your room-temperature coconut milk is chunky, pour the whole can into a saucepan and place over low heat. Stir until it's smooth and well-combined. Measure out what you need and proceed with the recipe. Save the remaining coconut milk to make paleo ganache.
• Water adds additional moisture to the batter.
• Eggs help lift and set the batter. I don't recommend swapping them out if you can help it. But if you're allergic, you could try some combination of applesauce, flax or chia egg, aquafaba, or Just Egg. 
• Oil adds moisture and keeps the cupcakes soft when chilled. I've tested this with grapeseed oil and sunflower oil which work equally well. Paleo-friendly options are avocado oil or mild olive oil.
• Maple syrup sweetens the cupcakes. I like the flavor that darker syrup adds here, but any grade will work. As always, use 100% real maple syrup. The consistency of the maple syrup is important for the texture of the cake, so try not to swap it for another liquid sweetener if you can help it. That said, agave syrup would be the closest in terms of moisture content and sweetness level. Or you could use honey thinned with a little hot water or coconut sugar liquified into a syrup. For keto coconut flour chocolate cupcakes, you could try maple-flavored monkfruit syrup.
• Baking powder and baking soda lift the batter, making it light and airy. Be sure both are fresh and perky for the best lift. 
• Salt sharpens the flavors. I use fine sea salt, but kosher salt will also work. Avoid table salt, which can taste harsh.

How to Make Coconut Flour Chocolate Cupcakes

This easy coconut flour chocolate cupcake recipe takes just 10 minutes of prep time and 20 minutes of baking, plus some inactive time for letting the cupcakes cool before topping them with the coconut milk ganache.

This recipe makes 12 cupcakes. You can double or triple the recipe for more cupcakes! If a layer cake is what you're after, see this coconut flour chocolate cake recipe; same batter, different pan!

Tips for Baking the Moistest Coconut Flour Chocolate Cupcakes

A few techniques for foolproof cupcakes every time.

• Use weight measurements if possible. It's more accurate and so much easier, with fewer dishes to wash. This is my favorite kitchen scale.
• Use the ingredients called for here if possible. I tested this chocolate coconut flour cupcake recipe many times to get it just right with these ingredients, so I recommend trying it as written before making any tweaks. However I gave my best guesses for ingredient swaps above!
• Be sure to combine the coconut milk first (see note). It separates into thick cream and watery goo as it sits, and we want creamy, homogenous milk for the best results.
• Take care not to overbake. When the cupcakes are done, the tops should spring back to the touch, and a toothpick inserted near the center should come out with a few moist crumbs – no wet batter and not completely clean.
• Be sure to let the cupcakes cool completely before topping them with ganache. We don't want to melt the ganache on warm cupcakes! If you need to speed this up, you can pop the cupcakes in the fridge once they've cooled down a little.
• The cupcakes are best served at room temperature when the cake and ganache are soft. The ganache will harden if refrigerated.

Coconut Flour Chocolate Cupcakes for Everyone

These coconut chocolate cupcakes are like a sophisticated take on classic chocolate cupcakes, with rich bittersweet chocolate notes, addictively moist and squidgy middles, and swirls of luxurious chocolate ganache.

I brought these to my brother's family and they were loved by children and adults alike. In fact my youngest niece (Nora, age 7) demanded a second one. Granted, the kids in my family have refined tastebuds, but still.

I hope you love these moist and fudgy coconut flour chocolate cupcakes as much as my family does!

*Bojon appétit! For more Bojon Gourmet in your life, follow along on Instagram,  Facebook, or Pinterest, purchase my gluten-free cookbook Alternative Baker, or subscribe to receive new posts via email. And if you make this coconut flour chocolate cupcake recipe, I’d love to know. Leave a comment and rating below, and tag your Instagram snaps @The_Bojon_Gourmet  and  #bojongourmet.*

5 from 6 reviews

Fudgy Coconut Flour Chocolate Cupcakes

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These coconut flour cupcakes are loaded with rich cocoa flavor, and they're unbelievably moist and tender. Easy to make in one bowl in about 30 minutes. Allergy-friendly and free of dairy, gluten, grains, nuts, and refined sugar – though your guests will never know!

Top them with a double or triple batch of coconut milk chocolate ganache for an extra-chocolatey treat.

Alanna Taylor-Tobin

Prep Time: 10 minutes minutes

Cook Time: 20 minutes minutes

Total: 30 minutes minutes

Servings: 12 cupcakes

Ingredients

• 1-3 recipes vegan chocolate ganache*
• 1 teaspoon coconut oil, for the pan

Wet Ingredients

• 2 large eggs (about 100 grams out of the shells)
• ¼ cup + 2 tablespoons (78 g) neutral oil (grapeseed, sunflower, avocado, or mild olive oil)
• ¾ cup (240 g) maple syrup (preferably dark colored)
• ½ cup (115 g) full-fat canned coconut milk*
• 2 tablespoons (30 g) water
• 2 teaspoons vanilla extract

Dry Ingredients

• ½ cup (50 g) Dutch-process cocoa powder (such as Rodelle organic)
• ½ cup (60 g) Bob’s Red Mill coconut flour
• ¼ cup (30 g) Bob’s Red Mill tapioca flour
• 1 ½ teaspoons baking powder
• ¼ teaspoon baking soda
• ½ teaspoon fine sea salt

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Instructions

Prepare Things

• Make the ganache and let it sit at room temperature to thicken while you make the cupcake batter (at least 30 minutes and up to 24 hours in advance).
• Position a rack in the center of the oven and preheat to 350ºF.
• Line a standard-sized muffin tin with paper liners.

Make the Batter

• In a large bowl, combine the eggs and oil. Whisk until smooth and emulsified. Whisk in the maple syrup, then the coconut milk, water, and vanilla.
• Place a medium mesh strainer over the bowl (or over a separate bowl if it's easier) and sift in the cocoa powder, coconut flour, and tapioca flour with the baking powder, baking soda, and salt. Whisk the flours into the wet ingredients until very smooth. If there are some lumps in the batter, let it sit for a minute or two, then whisk again. The batter will start out very thin, but it will thicken up as the flours begin to absorb moisture.
• Divide the batter between the muffin cups, filling them about two-thirds of the way.

Bake

• Bake the cupcakes until the top a toothpick inserted near the center comes out with moist crumbs, 15-20 minutes.
• Let the cakes cool in the pans for 15 minutes, then remove them to a wire rack and let cool completely, about 20 more minutes.

Finish

• If the ganache is very loose, pour it over the tops of the cupcakes.

  If the ganache is more firm, swirl it over the cupcakes.

  If the ganache is firm enough, use a piping bag fitted with a large star tip and pipe it over the tops of the cupcakes.
• Serve right away, or store at room temperature for a up to an hour (after that, you'll want to place the cupcakes in a covered container so they stay moist).
• The cupcakes are best within 1-2 days of baking, but leftovers keep beautifully, refrigerated airtight, for up to 5 days. Or freeze leftovers for up to 1 month. Bring to room temperature before enjoying.

Notes

*How much ganache you need will depend on how you decide to top the cupcakes. For piping, make a triple batch (you may have some leftover which you can roll into truffles or use for another project). For pouring or spreading the ganache, 1-2 batches will be enough. 

Make-ahead options:

• The cupcakes can be made 1 day ahead, covered, and stored at room temperature. Or refrigerate for up to 2 days ahead. Or freeze airtight for several months.
• The ganache can be made 24 hours ahead and stored at cool room temperature, or refrigerated for up to 1 week. Warm the chilled ganache before using to make it spreadable again.

Making this? I'd love to see!Tag your snaps @The_Bojon_Gourmet and #bojongourmet!