Preheat the oven to 350 F. In a medium bowl, whisk together flour, salt, and baking soda. In a large bowl, mix together butter, peanut butter, granulated sugar and brown sugar until fluffy.
Add in the egg and vanilla extract and mix until smooth. Add in the flour mixture, and mix until it is fully combined. Divide the cookie dough into two bowls. Add in green food coloring to one bowl and blue to the other.
Take a small amount of each cookie dough and roll together into a ball. Flatten slightly and place one peanut butter cup in each cookie dough. Roll into a ball and place onto a ungreased baking sheet at least 2-inches apart. Bake for 10-12 minutes.