Preheat the oven temperature to 350°F (175°C) and line a 8x8-inch baking pan or 8x8 square cake pan with parchment paper. For easy removal and cleanup, give the pan a light spray of cooking spray as well.
Melt butter in microwave for about 30 seconds. Then stir in the brown sugar and coffee. Put back in microwave for an additional 30 seconds. Remove and stir. This mixture should have a shiny appearance. If mixture is not fully melted, add back to microwave for 30 seconds. Once you reach the glossy appearance set aside and let cool for two minutes.
Once butter is cooled add in the two eggs and whisk until fully incorporated.
Whisk together the dry ingredients: In a separate bowl, sift the whole wheat pastry flour, baking powder, baking soda, cocoa powder and salt.
Add the dry ingredients to the wet ingredients and stir until just combined. Don't overmix, best to use a danish whisk! You want the batter to stay dense and fudgy.
Stir chocolate chunks into brownie batter for that extra chocolaty goodness. If you want your brownies to have a more intense chocolate flavor, feel free to add even more chocolate chips (or chunks).
Pour batter into your prepared pan and smooth it into an even layer.
Bake for 30-35 minutes. The best way to check if they are ready is to use an internal thermometer. It should reach 190 F for the perfect bake. This may seem soft but will result in a perfectly fudgy brownie.
Cool in the pan for 10–15 minutes, then remove from the pan and let it cool completely before cutting into squares.