At least 12 hours before baking the muffins, combine sourdough starter, yogurt, and flour in a medium bowl. Cover and place in a warm place to culture for 12-24 hours.
Preheat oven to 375°F.
Combine cinnamon, sea salt, baking soda, and baking powder together with a fork in a small bowl.
In a separate bowl beat eggs; whisk in butter, honey, and pumpkin puree.
Sprinkle dry ingredients over soured dough. Pour in wet ingredients slowly while combining. When almost all of the liquid has been used, sprinkle the chocolate chips over the batter and stir in with the remaining liquid ingredients.
Spoon batter into muffin cups until nearly full.
Bake 20-25 minutes or until a toothpick inserted into the center of a muffin comes out clean.