Update on 3/15/2025: I've tested this recipe with the addition of baking powder and it works quite well and the cupcakes rise more than without it. I've added the recipe using baking powder below this one. I use 2 tablespoons of coconut milk for this cupcake recipe to make it a more tender muffin. You can use any dairy or dairy-free milk. I recommend parchment cupcake liners or silicone muffin liners for all cupcakes made with coconut flour and I know some readers also grease the liners. If you'd like to reduce or replace the oil or butter in this recipe, you can replace all or part of it with an equal amount of applesauce.For SCD, use honey only.The Keto version can be found in my Everyday Keto Baking cookbook. Or, replace the honey with a low-carb sweetener. See my book for more details.
Preheat your oven to 350°F (175°C, or gas mark 4).
Combine all the dry in ingredients, except for the vanilla seeds, and blend well.
Add the wet ingredients to the dry ingredients and use a mixer to blend well. You can use a food processor, hand or standing mixer to get it well-blended. Let the batter sit for a few minutes and mix once more. Optionally, add the vanilla beans and blend well. The batter is thin.
Fill cupcake liners about ¾ of the way with batter.
Bake for about 20 minutes or until a toothpick inserted in the center of a cupcake comes out clean.
Cool and then frost.
Store covered for a few days at room temperature, or the refrigerator for a few weeks, or freeze for a few months.