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.
Add 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.
*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.