Preheat oven to 350 degrees and prepare a muffin pan with liners. Set aside.
Combine flour, salt, baking soda, baking powder, and cinnamon in a medium bowl. Set aside.
In another bowl combine almond milk, apple cider vinegar, coconut sugar, pumpkin puree, and coconut oil.
Make a well in the middle of the flour and pour in wet ingredients. Stir just to combine.
Scoop ⅓ of batter into another bowl, add cocoa powder and stir again just to combine.
Spoon a bit of the pumpkin batter into muffin wells followed by a small bit of the chocolate. Continue this process alternating between the two batters to create layers.
Use a toothpick or skewer to gently swirl the layers.
Lift pan and drop from a few inches in the air on to the counter. This will release air bubbles and level the batter.
Bake in preheated oven for 27-29 minutes or until a toothpick inserted comes out clean.
Leave muffins in the pan to cool for 5 minutes before removing and placing on a cooling rack to continue to cool.