Place a rack in the center of your oven and preheat the oven to 350°F. Line an 8x8-inch baking pan with parchment paper so that the paper overhangs 2 opposite sides like handles. Lightly coat the paper with non-stick spray. Set aside.
In a large mixing bowl, stir together the all-purpose flour, white whole wheat flour, granulated sugar, cocoa powder, baking powder, and salt until well combined.
Add the applesauce, coffee, canola oil, and vanilla. Whisk until smoothly combined.
Fold in the chocolate chips.
Scrape the batter into the prepared pan and smooth the top. Bake the brownies for 15 minutes, until the edges are set, the center looks slightly underbaked, and a toothpick inserted in the center comes out without any wet batter clinging to it (a few moist crumbs are fine). Place the pan on a wire rack and let cool for at least 1 hour (these actually taste even better refrigerated overnight if you can stand the suspense). Lift onto a cutting board using the parchment handles. Slice and serve.
Notes
TO STORE: Store brownies in an airtight container at room temperature for up to 3 days. You can also store them in the refrigerator for up to 5 days.
TO FREEZE: Place brownies in an airtight, freezer-safe storage container in the freezer for up to 3 months. Let thaw in the refrigerator overnight.