During the administration of President Corazon Aquino, he was appointed as the Director of the National Bureau of Investigation (NBI).
In 1992, he ran as mayor of Manila and won, serving two terms until 1998.
He made an unsuccessful bid to the presidency in 1998.
Two years later, in 2000, he was appointed by President Joseph Estrada as the Secretary of the Department of the Interior and Local Government (DILG).In 2001, he ran again for mayor of Manila but lost to then incumbent Lito Atienza.
During the 2004 elections, he ran for senator and won.
Three years later, in 2007, he decided not to finish his term in the Senate and ran again for mayor of Manila.
He lost his bid for a fifth non-consecutive term to Estrada in 2013 and 2016.
He failed to win and lost to his former Vice Mayor Isko Moreno in another comeback bid in 2019.
Due to his tough stance against suspected criminals, Lim was able to earn the nickname “Dirty Harry”.