Preheat the oven to 375 degrees F. Line a 12-cup cupcake pan with paper liners and set aside.
In a small bowl, combine the chopped pecans, melted butter, brown sugar, cinnamon, nutmeg and pinch of salt. Set aside.
In a large bowl, sift together the flour, sugar, cocoa powder, baking powder, baking soda, and salt. Add the chocolate chips and stir to combine.
In a small bowl, whisk the eggs. Add the milk and vegetable oil then whisk until smooth. Pour the egg mixture into the flour mixture and stir until just combined.
Evenly pour the batter into the prepared paper liners. Each muffin cup should be filled ⅔ to the top. Bake for 2 minutes then remove the muffin pan from the oven and working quickly, spoon some of the pecan mixture into the center of each muffin. Return the pan to the oven. Continue to bake for 16-20 more minutes, or until a toothpick inserted into the muffin comes out with just a crumb or two.
Let the muffins cool in the pan for 5 minutes then move the muffins to a cooling rack until completely cooled.
Recipe by Lemon & Mocha at http://www.lemonandmocha.com/2018/11/02/double-chocolate-pecan-muffins/