01 - In a medium saucepan, melt the butter over medium heat, swirling often, until foamy and deep golden with a nutty aroma, 5–7 minutes. Immediately transfer to a large mixing bowl and let cool 10 minutes.
02 - Whisk honey, brown sugar, and granulated sugar into the cooled brown butter until smooth. Whisk in eggs and vanilla extract until the mixture is glossy and homogenous.
03 - In a separate bowl, whisk together flour, baking soda, baking powder, and salt. Gradually mix dry ingredients into the wet mixture, blending until just combined.
04 - Gently fold chocolate chips and chopped pretzels into the dough until evenly distributed.
05 - Cover the dough and refrigerate for at least 30 minutes, or up to 24 hours for deeper flavor and better texture.
06 - Preheat oven to 350°F (175°C). Line two baking sheets with parchment paper.
07 - Scoop 2-tablespoon portions of dough onto prepared sheets, spacing each about 2 inches apart. Sprinkle tops with flaky sea salt, if desired.
08 - Bake for 11–13 minutes, until edges appear golden brown and centers remain slightly underbaked.
09 - Let cookies cool on the baking sheet for 5 minutes, then carefully transfer to a wire rack to cool completely.