jetBlue previously had its headquarters at 80–02 Kew Gardens Road, and then in the Forest Hills Tower, both in Forest Hills, Queens, New York City, 6 miles (9.7 km) from the current office in Long Island City. In 2001 the airline had announced that it wanted to take 74,000 square feet (6,900 m2) of space in the Forest Hills Tower, and by December 2002 announced that it planned to increase its leased space.
On October 22, 2008, jetBlue opened its new primary hub at John F. Kennedy International Airport (JFK), Terminal 5, or simply T5. The mostly new terminal, costing approximately $800 million, partially encircles the historic TWA Flight Center, the former Trans World Airlines terminal designed by Eero Saarinen, which remains closed. According to the plan, passengers will eventually be able to check in for flights in the landmark building, then transfer to the new structure via the original passenger departing-arrival tubes from Saarinen's original terminal and its 1969 addition by Roche-Dinkeloo.
In March 22, 2010, jetBlue turned down incentives from the City of Orlando and announced its headquarters would keep its Forest Hills office, start leasing and using a new office in the Brewster Building in Long Island City, New York. in Queens Plaza in Long Island City, move its headquarters there in mid-2012, and start a joint branding deal with New York State using the iconic I Love NY logo.
In December 2006, jetBlue, as part of their RTP plan, removed a row of seats from their A320s to lighten the aircraft by 904 lb (410 kg) and reduce the cabin crew size from four to three (per FAA regulation requiring one flight attendant per 50 seats), thus offsetting the lost revenue from the removal of seats, and further lightening the aircraft, resulting in less fuel burned.
On June 22, 2009, Frontier Airlines announced that pending bankruptcy court approval, Republic Airways Holdings, the Indianapolis-based parent company of Republic Airlines, would acquire all assets of Frontier Airlines for the amount of $108 million. Thus, Frontier Airlines would become a wholly owned subsidiary of Republic. However, 5 weeks later on July 30, Dallas-based Southwest Airlines announced that it would be making a competing bid of $113.6 million for Frontier with intentions to also operate Frontier as a wholly owned subsidiary, but that it would gradually fold Frontier resources into current Southwest operating assets.
While its financial performance started showing signs of improvement, in February 2007, jetBlue faced a crisis, when a snowstorm hit the Northeast and Midwest, throwing the airline's operations into chaos. Because jetBlue followed the practice of never cancelling flights, it desisted from calling flights off, even when the ice storm hit and the airline was forced to keep several planes on the ground. Because of this, passengers were kept waiting at the airports for their flights to take off. In some cases, passengers who had already boarded their planes were kept waiting on the apron for several hours and were not allowed to disembark. However, after all this, the airline was eventually forced to cancel most of its flights because of prevailing weather conditions. The fiasco reportedly cost JetBlue $30 million.
In May 2015, Indigo and Frontier announced the departure of David Siegel as CEO. He had already previously turned over the role of president to Barry Biffle, formerly of Spirit Airlines. Siegel was not immediately replaced. Instead, his duties were split between Biffle and Indigo chairman Bill Franke. Biffle cited operational issues in connection with Siegel's departure.
In May 2017, Allegiant Air took delivery of its first brand-new A320. Allegiant took delivery of ten new A320s in 2017 and is scheduled to accept two in 2018. All new aircraft will be painted in Allegiant's new livery at the time it is delivered. Older Airbus aircraft will be repainted during their C-checks. The new Airbus aircraft will have fuel-efficient sharklets. The new A320s seat 186 passengers, an increase of the 177 seats that are found in the rest of the Allegiant A320 fleet. To fit the additional nine seats, Allegiant opted for the Airbus Space-Flex V2 Lavatory. 
Like Ryanair, the low-cost airline founded by the Ryan family of Ireland, who also have invested in Allegiant, the airline seeks ancillary revenue to supplement ticket revenue. These ancillary fees include those for checking luggage, carrying on luggage (other than a small personal item), buying food and drinks on board, obtaining advance seat assignments, and more. Allegiant CEO Maurice Gallagher said in 2009, "We collect $110 from you at the end of your trip. If I tried to charge you $110 up front, you wouldn't pay it. But if I sell you a $75 ticket and you self-select the rest, you will."
On April 10, 2008, Frontier filed for Chapter 11 bankruptcy in reaction to the intent of its credit card processor, First Data, to withhold significant proceeds from ticket sales.[better source needed] First Data decided that it would withhold 100% of the carrier's proceeds from ticket sales beginning May 1. According to Frontier's press release, "This change in practice would have represented a material change to our cash forecasts and business plan. Unchecked, it would have put severe restraints on Frontier's liquidity..." Its operation continued uninterrupted, though, as Chapter 11 bankruptcy protected the corporation's assets and allowed restructuring to ensure long-term viability. After months of losses, Frontier Airlines reported that they made their first profit during the month of November 2008, reporting US$2.9 million in net income for the month.
On July 1, 2010 Allegiant returned to Long Beach Airport (LGB) in Long Beach, California having previously served LGB with DC-9 jets with nonstop flights to Las Vegas (LAS) and Lake Tahoe (TVL) in 2000. The airline also intended to fly from Bellingham International Airport and Stockton several times a week; however, there is no service at present flown between these two cities although Allegiant continues to serve Stockton with flights to Las Vegas, Phoenix/Mesa and San Diego. In November 2011, Allegiant closed its Long Beach facility and consolidated all Los Angeles area flights at Los Angeles International (LAX).