Bring quinoa and water to a boil in a heavy saucepan set to medium-high heat. Cover, reduce heat to low and cook for 10 minutes. Turn off heat and let sit, covered, for 10 minutes more. Fluff with a fork and transfer to the refrigerator to cool.
Preheat oven to 350 degrees F. Line muffin pan with 12 muffin tins.
Add milk, eggs, vanilla extract, almond extract, and coffee to a food processor. Blend to combine. Add 2 cups cooled quinoa and melted butter. Blend until smooth. Add sugar, cocoa powder, baking powder, baking soda and salt and blend until combined. Fold in butterscotch chips.
Evenly distribute in each of the dozen muffin liners and transfer to the oven to bake for 30 minutes or until a toothpick inserted into the center comes out clean. Let cool for a few minutes. Transfer to a baking rack to cool completely, or enjoy warm.