Preheat and prep. Heat the oven to 350°F (175°C). Line a standard 12-cup muffin pan with liners or lightly grease each cup.
Whisk the dry ingredients. In a large bowl, whisk together amaranth flour, oat flour, almond flour, baking powder, baking soda, salt, cinnamon, ginger, and nutmeg until no clumps remain.
Combine the wet ingredients. In a separate bowl or large measuring cup, whisk pumpkin puree, eggs, maple syrup, oil, milk, and vanilla until smooth. If using flax eggs, let the mixture sit 5 minutes to thicken before adding.
Bring it together. Pour the wet mixture into the dry.
Stir gently with a spatula until just combined. Do not overmix; a few streaks are fine.
Fold in extras. Add nuts, chocolate chips, or cranberries if using. Fold lightly to distribute.
Fill the tin. Divide batter evenly among the muffin cups, about 3/4 full. Sprinkle with pepitas or turbinado sugar if you like a little crunch.
Bake. Bake for 18–22 minutes, or until a toothpick comes out with a few moist crumbs and the tops spring back gently when tapped.
Cool. Let muffins cool in the pan for 5 minutes, then transfer to a rack to cool completely.
This helps set the crumb and prevents sogginess.