Preheat your waffle baker according to manufacturer's instructions. Using a medium sized mixing bowl, whisk together the flours, flaxseed meal, baking soda, baking powder, salt and sugar. Using a smaller separate mixing bowl, beat together the eggs and melted butter, then add the yogurt, almond milk and pure almond extract. Mix together until well blended. Add the chocolate chips and mix again one more time. Do not over mix.
Add the wet ingredients into the dry flour mixture and stir until combined. Let the batter rest for about 5 minutes.
When your waffle baker is ready, spray with non-stick spray and, using a ladle, or something with a spout, pour in your waffle batter, start with just a 1/3 cup (depending on what size your waffle baker is). Close the waffle baker and flip (if you have a waffle baker that has two sides) and repeat. Press the timer and cook for about 2 to 2.5 minutes, or until the waffles are golden on both sides and cooked through.
Serve warm with maple syrup and top with the walnuts! Enjoy!