Preheat oven to 350F and line a 13x9-inch baking pan with parchment paper.
In a large bowl, whisk together flours, granulated sugar, and salt. Cut in butter until mixture is crumbly.
Press mixture firmly into the bottom of the prepared pan.
Bake for 15-18 minutes or until lightly brown.
For the Filling
In teh same bowl, whisk together brown sugar and next 4 ingredients until combined.
Stir in pecans and chocolate chips, and pour over the prepared crust.
Bake for 30 to 40 minutes or until center is set. Let cool completely. Remove from pan and cut into bars. Store in an airtight container for up to 5 days.