Preheat oven to 350 degrees and line a baking sheet with parchment paper.
In a sauce pot over medium heat, add the butter. Stirring constantly, cook the butter until it browns, about 8 minutes. The butter will smell nutty and have an amber color. Pour the butter into a large bowl and let cool for 15 minutes.
When the butter has cooled, add the sugars. Using a hand mixer, beat the butter and sugars (starting on low and then increasing speed) for 2 minutes.
Add the eggs and vanilla and beat until light and fluffy, about 2 minutes.
In a small bowl, whisk together the flour, baking soda, and salt.
Add half of the flour mixture to the wet ingredients and beat until incorporated. Add the other half and beat until just combined.
Stir in the caramels chips and chopped chocolate in by hand. Using a tablespoon cookie scooper, scoop a heaping tablespoon of dough and place it onto the baking sheet. Leaving 3 inches of space between cookies, scoop more dough onto the baking sheet.
Stuff 3 mini pretzels (or as many as you can) into each cookie dough ball. Bake for 9-11 minutes until the edges are golden and the middles are still soft. When fresh out of the oven, sprinkle the tops with some flaky sea salt.
Leave the cookies to sit on the warm baking sheet for 10 minutes before removing to a cooling rack. Store leftovers in an air-tight container for up to 1 week. Enjoy!