He won a seat in the Makati City Council for the first district in 1998. Among Puno's notable ordinances filed during his first term was the installation of a surveillance camera in every convenience store in Makati that operates 24 hours a day, as protection against robbers who prey on convenience stores. He left the city council after his third and final consecutive term ended in 2007. His seat in the city council was kept by his eldest daughter, Tosca Camille. Three years later, he teamed up with Junjun Binay to run for vice mayor of Makati. Although Binay won the mayoralty race, Puno lost to Romulo "Kid" Peña Jr., who was the running mate of then-outgoing vice mayor Ernesto Mercado.