Preheat the oven to 350 degrees.
In a large bowl or a stand mixer, add the sourdough discard, flax, melted vegan butter, plant milk, and sugar. Beat until combined.
In a separate bowl, whisk together the flour, cinnamon, baking soda, salt, and ground nutmeg.
Sprinkle into the large bowl with the wet ingredients. Beat only until combined—about 30 seconds. Do not over mix.
Add in the chocolate chips (or ⅓ cup of any other fillings you desire). Fold into the batter using a rubber spatula for another 30 seconds—only until the ingredients are combined. Again, do not over mix.
Line a muffin tin with liners or silicone muffin cups. Scoop the batter evenly into the 12 cups—it should fill between ½ and ¾ of each cup.
Bake in the oven for 20 minutes, or until a toothpick comes out clean.