Prospero's career in politics began in 1963 with his election as a Nabunturan city council member. He was elected the Mayor of Nabunturan in 1972, an office he held for 14 years. He also served as the mayor of New Corella early in his career. Amatong was elected the Governor of Davaodel Norte, which consisted of 21 towns, in 1992. As governor, Amatong spearheaded the creation of a new province Compostela Valley, which consists eleven municipalities which were formerly part of Davao del Norte. Amatong became the interim governor of the newly created Compostela Valley province for three months in 1998. He was later elected to the House of Representatives of the Philippines, representing Compostela Valley's second congressional district as a congressman. Amatong remained in Congress until his retirement in 2007. His son, Rep. Rommel Amatong, was elected as his successor in the district in 2007. Throughout his long political career, no complaints were ever filed against him by the Ombudsman. Politicians from both Davao del Norte and Compostela Valley continued to consult Amatong following his retirement, earning him the nickname as the "grand old man" of Davao politics.
Personal life
Prospero Amatong suffered a fall in a New York City park in May 2009 while on vacation with his wife, Luz, their children and other family members. He was hospitalized with head injuries, leaving him in a coma. Amatong died in a New York Cityhospital on May 16, 2009, at the age of 77. His body was flown back to the Philippines for burial. Tributes poured in following news of Amatong's unexpected death. Compostela Valley Governor Arturo Uy called Amatong, "...exceptional as a leader, a master politician. I would say no one could ever duplicate his performance in our lifetime. He is the real Mr. Service." Laak Mayor Reynaldo Navarro referred to Amatong as, "a legend, a real champion who has never tasted defeat." Former Davao del Norte Vice Governor Victorio Suaybaguio Jr., a friend of Amatong during his governorship, spoke of him, "am saddened by the death of a great man whose life was dedicated to mankind. It's a loss to all of us. My prayers to the bereaved family. Farewell my brother." Davao del Norte Gov. Rodolfo del Rosario also sent condolences to Amatong's family.