Preheat oven to 350°F. Prepare a standard 12 cup muffin tin with paper liners and spray with nonstick cooking spray in each liner.
In a large bowl, combine the flour, cocoa powder, sugar, baking powder, baking soda, salt and cinnamon.
In a medium bowl, combine the pumpkin, vanilla, almond milk, egg and yogurt. Pour mixture into the flour mixture and stir until just combined.
Gently fold in the chocolate chips. Fill prepared muffin tin ¾ full of batter.
Bake for 20-25 minutes, until a toothpick inserted in the center comes out clean.
Allow muffins to cool in tin, then remove to a wire rack to continue cooling. Prepare a cooled muffin tin with paper liners and cooking spray, then fill with the remaining batter and bake, just as before.
Serve and store leftovers in an airtight container.