Preheat the oven to 350ºF and line a muffin tin with liners. Spray the liners with cooking spray for easy removal.
In a medium bowl, mix the dry ingredients (except cocoa powder and chocolate chips).
In a large bowl, whisk eggs, then add maple syrup, 3/4 cup almond milk, and pumpkin puree. Mix well.
Combine dry ingredients with wet ingredients, then add melted coconut oil and mix.
Set aside 1/2 cup of batter without cocoa powder.
Add cocoa powder, chocolate chips, and remaining 1/4 cup almond milk to the bowl. Mix until combined.
Fill each muffin cup 3/4 full with chocolate batter. Top with a teaspoon of non-chocolate batter.
Swirl the layers together with a toothpick or knife.
Bake at 350ºF for 18-22 minutes until fully cooked.
Let cool for 5 minutes before removing from the tin.