Preheat oven to 350°F. Line 2 cookie sheets with parchment or silpat baking mats.
Place chocolate chips and 1/4 cup peanut butter in a microwave safe bowl. Heat on high power in 30 second increments, stirring between each, until melted and smooth. Freeze for no more than 10-12 minutes, stirring every few minutes, until the mixture is stiff like a truffle mixture, but still able to scoop into balls. Scoop 1 tablespoon size balls of this mixture and place on a third cookie sheet lined with wax paper. Chill until ready to use. (Note: some of the chocolate may get hardened, so it might be crumbly. Use your hands to mold it into balls. It’s a little messy.)
Cream butter, 1/2 cup peanut butter, and both sugars in the bowl of an electric mixer fitted with the paddle attachment. Slowly mix in melted chocolate. Add egg, vanilla, milk, and salt, cocoa and baking soda. Mix until combined. Slowly add flour and mix until dough comes together.
Scoop 2 tablespoon sized balls of dough. Flatten each ball slightly and place one of the peanut butter chocolate balls inside, wrapping up the dough around them and rolling into a large ball. Make sure the cookie dough is sealed around the truffle or you'll get truffle spillage in the oven. Place on the prepared cookie sheets and press down slightly using the tines of a fork (there will be some resistance, they won’t really flatten because of the inside.)
Bake for 8-10 minutes, until they just begin to loose their glossy sheen. I like to under bake them, but if you like a more done cookie, you can bake them the full 10 minutes. Cool completely on cookie sheets.
If you eat these within a few hours of baking they’ll be gooey and drippy like the pictures. As the inside cools, it’ll be more like a truffle on the inside of the cookie.
Store in an airtight container for up to 3 days or freeze for up to one month.