Hurricane Andrew caused more than $20 billion in damage just south of the Miami-Dade area in 1992.

Several financial scandals involving the Mayor's office and City Commission during the 1980s and 1990s left Miami with the title of the United States' 4th poorest city by 1996. With a budget shortfall of $68 Million and it's municipal bonds given a junk bond rating by Wall Street, Miami became Florida's first city to have a state appointed oversight board assigned to it in 1997. In the same year, city voters rejected a resolution to dissolve the city and make it one entity with Dade County. The City's financial problems continued until political outsider Manny Diaz was elected Mayor of Miami in 2001.

Drug wars reached a peak in 1998, when the Liberty City area of Miami was the focal point of deadly battles between Anthony "Little Bo" Fail and the John Does, the largest gang in Miami at the time. This feud started when the leader of the gang, Curtis Silwa, was arrested; Fail saw as an opportunity to take control of the gang and reclaim revenue from drug sales.

The Elián González uproar was a heated custody and immigration battle in the Miami area in 2000. The controversy concerned six-year-old Elián González, who was rescued from the waters off the coast of Miami. The U.S. and the Cuban governments, his father Juan Miguel González, his Miami relatives, and the Cuban-American community of Miami were involved. The climactic stage of this prolonged battle was the April 22, 2000, seizure of Elián by federal agents, which drew the criticism of many in the Cuban-American community. During the controversy, Alex Penelas, the mayor of Miami-Dade County at the time, vowed that he would do nothing to assist the Bill Clinton administration and federal authorities in their bid to return the six-year-old boy to Cuba. Hundreds of protesters, many of whom were outraged at the raid, poured out into the streets of Little Havana and demonstrated. Car horns blared, demonstrators turned over signs, trash cans, and newspaper racks and some small fires were started. Rioters jammed a 10-block area of Little Havana. Shortly afterwards, many Miami businesses closed, as their owners and managers participated in a short, one-day boycott against the city, attempting to affect its tourism industry. Employees of airlines, cruise lines, hotels, car rental companies, and major retailers participated in the boycott. Elián González returned to Cuba with his father on June 28, 2000.

The controversial Free Trade Area of the Americas negotiations occurred in 2003. It was a proposed agreement to reduce trade barriers while increasing intellectual property rights. During the 2003 meeting in Miami, the Free Trade Area of the Americas was met by heavy opposition from anti-corporatization and anti-globalization protests.

On June 27, 2005, the popular ex-city commissioner Arthur Teele walked into the main lobby of the Miami Herald headquarters, dropped off a package for columnist Jim DeFede, and told the security guard to tell his wife Stephanie he "loved her" before pulling out a gun and committing suicide. His suicide happened the day the alternative weekly Miami New Times published salacious details of Teele's alleged affairs, including allegations that Teele had sex with a transsexual prostitute and used cocaine.[30] At the time, Teele was being investigated by federal authorities for fraud and money laundering for allegedly taking $59,000 in kickbacks to help a businessman get millions of dollars in contracts at Miami International Airport.Teele was suspended from his job in 2004 by Florida governor Jeb Bush after being arrested for trying to run a police officer off the road. Teele was also charged in December 2004 with ten counts of unlawful compensation on charges he took $135,000 from TLMC Inc., promising that it would be awarded lucrative contracts to redevelop neighborhoods in Miami. Teele was also found guilty in March of 2005 for threatening an undercover detective.

Miami Beach