In a medium saucepan, cover the beets with water by an inch. Place the pot over medium high heat and bring the water to a boil. Reduce the heat to medium and simmer the beets until they are soft enough to easily be pierced through the center with a knife, about 25 minutes. Drain the beets and puree them. You may need to add a tablespoon or two of water to the beets to get them to puree smoothly, Add only what you need. Set the beet puree aside to cool.
Preheat your oven to 350 degrees.
In a large bowl whisk together the eggs, oil, and sugars. Add the vanilla extract and beet puree and whisk to fully combine. Mix the flour, cocoa powder, baking powder and salt into the wet ingredients. Stir in the chocolate chips.
Pour the batter into a 9x13 inch baking pan that has been sprayed with cooking spray or lined with foil or parchment. Bake for about 30 minutes or until a toothpick inserted into the center of the brownies comes out clean but still moist. Cool the brownies completely before cutting. They will keep in an airtight container for 3 days.