Arrange a rack in center of oven; preheat to 350°. Spray a 9" x 9" baking dish with cooking spray and line with parchment.

In a medium saucepan over medium heat, melt butter. Continue to cook, watching closely and stirring occasionally, until simmering and milk solids start to turn golden brown 7 to 8 minutes. Remove from heat. Add dark chocolate chips, almond extract, and ½ tsp. salt and stir until chocolate is melted and smooth.

Add granulated sugar and brown sugar and vigorously whisk until smooth (sugar won’t be completely dissolved). Let cool 5 minutes.

Add 1 egg and whisk to incorporate. Add remaining 1 egg and vigorously whisk about 10 seconds. Add flour and cocoa powder and fold with a rubber spatula until just combined. Coarsely chop 1 cup pistachios and fold into batter. Spread in prepared pan.

Bake brownies until a tester inserted into the center comes out clean, 20 to 22 minutes. Let cool.

Meanwhile, fill a small bowl with ice water. Wipe out saucepan. Fill saucepan halfway with water and bring to a boil. Add ½ cup whole pistachios and remove from heat. Let soak 1 minute, then transfer to ice water.

Using a slotted spoon, transfer pistachios to a clean kitchen towel and rub to loosen and remove skin. Transfer pistachios to a food processor and pulse until broken down into tiny pieces, about 2 minutes. With the motor running, slowly stream in 2 Tbsp. water and blend until smooth.

Transfer pistachio paste to a medium heatproof bowl. Add white chocolate chips, cream, and remaining ¼ tsp. salt. Microwave in 15-second increments, stirring between each, until melted and smooth, about 45 seconds total. Refrigerate until ready to use.

Spread ganache over brownies. Top with chopped pistachios.