On June 12, 2010, Spirit grounded its flights when its unionized pilots walked out on strike, stranding thousands of passengers. At that time, Spirit pilots were among the lowest-paid Airbus pilots in the United States. In May 2009, after more than four years of inconclusive negotiations between the airline and the Air Line Pilots Association (ALPA), Spirit pilots overwhelmingly (98% of votes) voted in favor of strike action over compensation, work rules, and benefits. In September 2008, Spirit began placing advertisements on the side of aircraft, overhead bins, tray tables, seatback inserts and bulkheads. On June 3, 2008, Spirit Airlines made a WARN (Worker Adjustment and Retraining Notice) application to potentially relocate or lay off hundreds of pilots and flight attendants, and the closure of their San Juan and LaGuardia crew bases. In 2006, Spirit exercised options to order 30 Airbus A320-200 aircraft for further expansion. Spirit also began service to Grand Cayman, San Francisco, and Boston in 2006, and in 2007 filed DOT applications to offer service to Costa Rica, Haiti, the Netherlands Antilles and Venezuela. In the fall of 2003, Spirit resumed flights to Washington, D.C.'s Ronald Reagan Washington National Airport, which were suspended after the September 11 attacks. In November 2001, Spirit inaugurated service to San Juan, Puerto Rico, and implemented a fully integrated Spanish-language customer service plan including a website and dedicated reservation line. Discrepancies were found in the marking and placarding of emergency equipment, passenger seats, storage areas and doors on eight of Spirit's DC9 and MD80 aircraft.

In 2000, the US Federal Aviation Administration (FAA) fined Spirit Airlines $67,000 for allegedly violating federal regulations on cabin and seat markings and placards. Prior to the decision to move the headquarters to Miramar, Spirit considered Atlantic City, New Jersey and Detroit, Michigan. It relocated its headquarters in November 1999, moving to Miramar, Florida, in the Miami Metropolitan Area. Spirit initially had their headquarters in Eastpointe, Michigan (formerly East Detroit) in Metro Detroit. At the time Spirit was utilizing DC-9 and MD-80 aircraft. In 1996, Janet Patton became Spirit Airlines' first woman pilot, and in 1998 she became the first woman captain. In response to criticism, Spirit Airlines said it would make sure all paid customers would always be able to fly to their destination, even if Spirit Airlines had to book them on a competitor's airline. The overbooking occurred because Spirit Airlines had given incorrect instructions to travel agents, causing those tickets not to be valid, even though the customers had paid for the flights. In the summer of 1994, Spirit Airlines overbooked flights, and 1,400 customers' tickets were canceled. During the next five years, Spirit expanded further, increasing service from Detroit and adding service in new markets such as Myrtle Beach, Los Angeles, and New York City. Flights between Atlantic City and Fort Myers, Florida, began on September 25, 1993. On April 2, 1993, Spirit Airlines began scheduled service to Orlando, Fort Lauderdale, and St. Scheduled flights between Boston and Providence began on June 15, 1992. Scheduled flights between Detroit and Atlantic City began on June 1, 1992. On May 29, 1992, Charter One brought jet aircraft into the fleet and changed its name to Spirit Airlines. In 1990, Charter One began scheduled service from Boston and Providence, Rhode Island, to Atlantic City. The airline service was founded in 1983 in Macomb County, Michigan, by Ned Homfeld as Charter One Airlines, a Detroit-based charter tour operator providing travel packages to entertainment destinations such as Atlantic City, Las Vegas, and the Bahamas. The company changed its name to Ground Air Transfer, Inc., in 1974. The company initially started as Clippert Trucking Company in 1964.

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