Preheat oven to 350°F (175°C). Line the bottom and sides of a 9-in (23 cm) square baking pan with parchment paper. In a large mixing bowl, mix together the flour, cocoa powder, brown sugar, and salt. Drizzle in the melted butter, then use a fork to mix the butter into the dry ingredients. (The crust mixture should hold together when pressed between two fingers.) Transfer the crust mixture to the prepared baking pan, then press down to form an even, thin crust. Bake for 15 minutes, then remove from the oven and set aside. Keep the oven on.
For the filling
In a large mixing bowl, whisk together the brown sugar, flour, and salt. Add the eggs, milk, vinegar, and vanilla extract, and whisk until smooth. Slowly whisk in the melted butter, then stir in the pecans.
Pour the filling over the pre-baked crust. The crust can and should still be warm. Sprinkle the chocolate chips over the top. Bake the bars for about 40 minutes, or until the filling is set around the edges and mostly set toward the center, with only a small section in the middle that is still slightly jiggly. The filling will continue to set as it cools.
Transfer the pan to a wire rack and let the bars cool completely in the pan, at least 2 hours. For the cleanest slices, refrigerate the bars for 1 hour before cutting. Slice into 16 bars.
STORAGE: Store the chocolate pecan pie bars in an airtight container at room temperature for up to 3 days, or refrigerate for up to 1 week. For the best texture, bring refrigerated bars back to room temperature before serving.
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