See this post for instructions on roasting a beet. Otherwise, you could sub another fruit puree, such as butternut squash or applesauce.
Preheat oven to 375 degrees F (190 C) and line 12 muffins with paper liners, or lightly grease (as original recipe is written // adjust number of muffins if altering batch size).
Prepare flax eggs in a large mixing bowl and let rest for 5 minutes.
Add beet puree, melted oil, maple syrup or agave, brown sugar, baking soda, salt and whisk for 45 seconds.
Stir in the almond milk and whisk once more.
Add cocoa powder and flours and stir with a spoon or spatula until just combined, being careful not to over-mix. If the batter appears too thick, add a touch more almond milk. But it should be quite thick and NOT pourable – rather, scoopable.
Lastly, stir in chocolate chips. Then divide batter evenly between muffin tins (should be enough for between 11-12 as original recipe is written) and sprinkle with a few more chocolate chips (optional but recommended).
Bake for 17-22 minutes or until a toothpick inserted into the center comes out clean. Let cool for a few minutes in the pan, remove from tins and let cool on a cooling rack. Will keep covered for several days. Freezer for longer-term storage.