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.
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.