Preheat your oven to 350°F (175°C). This ensures that your cookies bake evenly.
In a large bowl, whisk together the all-purpose flour, salt, baking soda, and baking powder. Set aside for later use.
In a separate bowl, beat the unsalted butter, light brown sugar, and granulated sugar together using an electric mixer until the mixture is light and fluffy, about 2-3 minutes.
Add the eggs one at a time, mixing well after each addition. Then, stir in the vanilla extract until fully incorporated.
Gradually add the dry ingredient mixture to the wet ingredients, mixing until just combined. Be careful not to overmix to avoid tough cookies.
Gently fold in the semi-sweet chocolate chips and Pretzel M&M's until evenly distributed throughout the cookie dough.
Using a cookie scoop or tablespoon, drop rounded balls of dough onto a prepared baking sheet, leaving enough space between each cookie to allow for spreading.
Before baking, sprinkle a pinch of sea salt on top of each cookie to enhance flavor and add crunch.
Bake in the preheated oven for 10-12 minutes, or until the edges are lightly golden but centers are still soft. Cookies will continue to bake on the sheet after removal.
Allow the cookies to cool on the baking sheet for about 5 minutes before transferring to a cooling rack to cool completely. Enjoy!