Prep the flax egg: Stir ground flaxseed with water in a small bowl. Let it thicken for 5 minutes.
Preheat and line: Heat the oven to 375°F (190°C).
Line a 12-cup muffin tin with liners or grease lightly.
Whisk dry ingredients: In a large bowl, whisk flour, brown sugar, baking powder, baking soda, salt, cinnamon, ginger, and nutmeg until no sugar clumps remain.
Add wet ingredients: To the same bowl, add pumpkin purée, non-dairy milk, oil, vanilla, and the flax egg. Stir gently until just combined. The batter should be thick and slightly lumpy.
Don’t overmix.
Fold in extras: If using chocolate chips or nuts, fold them in with a few quick strokes.
Fill the cups: Divide batter evenly among the muffin cups (about 3/4 full). Sprinkle with coarse sugar or pepitas if you like.
Bake: Bake 18–22 minutes, or until the tops spring back and a toothpick comes out clean or with a few moist crumbs.
Cool: Let muffins rest in the pan for 5 minutes, then transfer to a rack to cool. Enjoy warm or at room temperature.