Preheat the oven to 350 degrees.
Make the homemade caramel sauce: combine the coconut milk and coconut sugar in a small saucepan over medium-high heat. Bring to a slight boil and reduce heat to medium-low to simmer.
Stir in the coconut flour. Simmer for 20 minutes or until thickened by half, whisking frequently.
Remove from heat and stir in the vanilla and sea salt. Let cool slightly while you prepare the brownie batter.
Make the brownie batter: In a medium microwave-safe bowl, combine the chocolate chips and coconut oil. Microwave in 30 second increments, stirring in between until fully melted. Set aside to cool slightly.
In a stand mixer, beat the eggs and coconut sugar. Add vanilla, and chocolate + coconut oil mixture. Mix again to combine.
Sprinkle in the almond flour, cacao powder, coconut flour, baking powder, and salt. Mix until just combined.
Line a square baking dish with parchment paper and spray with cooking oil.
Pour about half of the brownie mixture evenly in to the bottom of the pan.
Cover with the homemade caramel sauce (if using store-bought use 1/2 cup).
Layer on the pecan halves evenly over the caramel.
Enclose the caramel and pecans with the rest of the brownie batter, carefully spreading the mixture across the top.
If needed, use a butter knife to spread it so the caramel and pecans do not get mixed in with the batter.
Bake for 30-40 minutes until it comes out clean with a toothpick. (Keep an eye on it- don't over bake!)
Let cool slightly then cut in to squares.