Preheat oven to 375°F. Line a muffin pan with paper liners or grease with nonstick spray.
In a medium bowl, combine flour, sugar, baking soda, baking powder, salt, and spices. Whisk together.
In a small bowl, combine eggs, pumpkin puree, milk, molasses, and vanilla extract. Whisk together. When well combined, whisk in coconut oil.
Pour pumpkin mixture into flour mixture and fold to combine. Add in mini chocolate chips and fold until incorporated.
Fill muffin cups 2/3 full. Sprinkle a few mini chocolate chips on top and press into batter a little.
Bake for 15 to 18 minutes. Cool and serve.