Preheat the oven to 350°F. Line a muffin pan with large paper liners.
In a medium bowl, whisk together the chia seeds and water. Set aside for a few minutes to thicken.
In a large bowl, whisk together the dry ingredients (spelt flour, pumpkin pie spice, baking soda, baking powder, and salt).
In the same bowl as the chia mixture, whisk together the wet ingredients (chia mixture, pumpkin puree, oil, maple syrup, brown sugar, and molasses) until smooth.
Add the wet mixture to the dry ingredients and stir until just combined. No patches of flour should remain. Be sure not to overmix the batter as spelt is a delicate flour. The batter will be thick.
If using, stir in the chopped walnuts. You can also reserve some for garnish on top.
Divide the batter equally between the 12 muffin liners. They should be about 3/4 full or a bit more. Add any reserved walnuts on top and gently push down (optional).
Bake the muffins for 20-24 minutes until a toothpick comes out clean.
Cool the muffins in the pan for 5-10 minutes, and then transfer each muffin onto a cooling rack until completely cool.
Serve and enjoy!