Preheat oven to 350 degrees F. Line a Baking sheet with parchment paper or coat with nonstick spray.
In a medium mixing bowl, whisk together the flour, baking powder, and baking soda.
In a large mixing bowl with an electric mixer, cream together the butter and sugars until light and fluffy. Be sure to scrape down the sides of the bowl with a rubber spatula. About 2-3 minutes.
Add in eggs and vanilla extract and continue to beat just until incorporated.
Slowly add in the dry ingredients and reduce the mixer speed. Beat together until combined and then add in the chocolate chips and pretzel pieces. Mix together until cookie dough has formed.
Scoop the cookie dough into balls with a mini ice cream scoop (equivalent to 2 tablespoons). Stuff each cookie dough ball with half of a caramel candy and be sure to cover it with dough by rolling the cookie. Be sure the caramel candy is not visible- otherwise it will easily melt through.
Top each cookie dough ball with a whole pretzel twist (optional). Then place the cookies on prepared baking sheets, be sure they are at least 2 inches apart. Bake for 9-11 minutes or until they are a light golden brown. Sprinkle with sea salt if desired. Let cool for a few minutes, then carefully transfer to a cooling wrack. The caramel inside will be very hot. Enjoy!