In a large bowl, add unsalted butter, granulated sugar, and brown sugar. Beat on medium speed until light and fluffy, about 3-5 minutes, stopping to scrape down the sides of the bowl periodically.
Add yogurt and pure vanilla extract, beat on medium speed until well combined.
Using a sifter or fine-mesh sieve, sift all-purpose flour along with baking soda and kosher salt. Mix on the lowest speed just until combined and no more flour pockets are visible. Avoid over mixing.
You can whisk the dry ingredients in a separate bowl and then add it to the mixture.
Add chocolate chips or chunks and chopped pecans (optional) and fold in gently.
Refrigerate the cookie dough, either by covering the bowl with cling wrap or drop spoonfuls of cookie dough on a rimmed baking tray lined with parchment paper and refrigerate for 2 to 24-48 hours. Cover the baking tray with plastic wrap to prevent the dough from drying out and absorbing odors.
Preheat the oven at 375° F for 10 minutes.
Remove the bowl from the refrigerator and let it sit on the counter for 10-15 minutes.
Scoop the cookie dough using a cookie scoop, roll between your palms to form a ball.
Top each cookie dough with more chocolate chips and bake at 375° F on the middle rack for 9-11 minutes (or a few minutes longer depending upon the size of the dough ball) until the edges turn golden brown and the centers remain soft.
If you chilled individual balls of cookie dough, transfer the dough balls to a baking sheet lined with parchment paper or silicon mat, leaving enough space between each ball of dough and bake. You can let it sit on the counter for 10 minutes to soften a bit or flatten them slightly so that they don’t stay dome-shaped. Follow baking instructions as mentioned above.
When the first batch is done, continue baking with the leftover batch of dough balls in the refrigerator. Make sure the baking tray has cooled down completely before placing the second batch.
Leave the cookies on the baking tray for 2 minutes, then transfer to a wire rack and let them cool completely.