Preheat oven to 375 degrees F (190 C) and line muffin tin with paper liners.
Prepare flax egg by mixing flaxseed meal and water in a large bowl - let rest for 5 minutes.
In the bowl with the flax egg, add the pumpkin puree, almond milk, lemon juice, brown sugar, oil, and vanilla extract and stir. Then add salt, baking soda and powder, and cinnamon and whisk.
Carefully place flours into a sifter and sift over wet ingredients and stir.
Add chocolate chips and stir again lightly until just incorporated. If the batter appears too thick, add a splash of almond milk or orange juice. Otherwise, you're ready to bake!
Spoon into paper-lined muffin tins (should be 11-12 as original recipe is written) until each liner is filled almost completely full (about 7/8ths). Sprinkle a few more chocolate chips on top for presentation (optional).
Bake for 22-28 minutes or until fluffy, golden brown and a toothpick inserted into the center comes out clean.
Let rest in the pan for 5 minutes, then transfer to a wire rack to cool completely. Store in an air-tight container or bag. Freeze for long-term storage.
Notes
*These muffins are very moist. If you prefer a more crumbly muffin, simply add a touch more flour and/or a handful of oats to absorb more of the moisture from the almond milk and pumpkin puree. *Right out of the oven, these can stick to the paper liner. I recommend letting them cool completely, covering them in a sealed container for a couple of hours and then trying again. They should come right loose! *Nutrition information is a rough estimate.