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

Combine flour, baking soda, baking powder, and sea salt in a medium bowl. Set aside.

Then, in the bowl of a standing mixer fitted with the paddle attachment, or in a large bowl with a hand-held mixer, beat the butter, granulated sugar and brown sugar on medium-high speed until light and fluffy, about1 minute.

Then, add the egg and vanilla and beat for an additional 1 minute.

Add the dry ingredients, beat on medium speed until combined.

Stir in the chocolate chips and pretzel pieces until evenly distributed throughout the dough.

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

Use a 2 Tablespoon cookie scoop to measure out portions of dough, roll them into balls and place them evenly spaced on the two baking sheets (about 8 per sheet). Repeat until all the dough is used.

Press one pretzel on the top before baking.

Bake in preheated oven for 9 to 11 minutes, or until the top is just set and the sides are just barely beginning to turn light golden brown.

Remove from oven and immediately sprinkle with flaky sea salt. Then, let the cookies cool on the baking sheet for 5-10 minutes.

After 5-10 minutes, transfer the cookies to a wire rack to cool completely.