Preheat your oven to 375 degrees Fahrenheit (190 degrees Celsius). Line two large baking sheets with silicone baking mats or parchment paper and set them aside.

In a medium bowl, combine flour, baking soda, baking powder, and sea salt. Set this mixture aside.

In a standing mixer or large bowl with a hand-held mixer, beat the softened butter, granulated sugar, and brown sugar on medium-high speed until the mixture is light and fluffy, about 1 minute.

Add in the egg and vanilla extract, beating for an additional minute.

Gradually add the dry ingredients to the wet ingredients and mix on medium speed until well combined.

Stir in the chocolate chips and broken pretzel pieces until everything is evenly distributed in the dough.

Transfer the cookie dough to an airtight container and chill in the refrigerator for at least 1 hour.

Using a 2 Tablespoon cookie scoop, measure out portions of the dough, roll them into balls, and place them spaced evenly on the baking sheets (about 8 cookies per sheet).

Press one pretzel on top of each ball before baking.

Bake in the preheated oven for 9 to 11 minutes, until the tops are set and the edges are lightly golden brown.

Remove from the oven and immediately sprinkle with flaky sea salt. Allow the cookies to cool on the baking sheets for 5-10 minutes, then transfer them to a wire rack to cool completely.