jetBlue experienced its first-ever quarterly loss during the fourth quarter of 2005 when the airline lost $42.4 million, enough to make them unprofitable for the entire year of 2005. The loss was the airline's first since going public in 2002. JetBlue also reported a loss in the first quarter of 2006. In addition to that, jetBlue forecasted a loss for 2006, citing high fuel prices, operating inefficiency, and fleet costs. During the first quarter report, CEO David Neeleman, President Dave Barger, and then-CFO John Owen released JetBlue's "Return to Profitability" ("RTP") plan, stating in detail how they would curtail costs and improve revenue to regain profitability. The plan called for $50 million in annual cost cuts and a push to boost revenue by $30 million. jetBlue Airways moved out of the red during the second quarter of 2006, beating Wall Street expectations by announcing a net profit of $14 million. That result was flat when compared to jetBlue's results from the same quarter a year before ($13 million), but it was double Wall Street forecasts of a $7 million profit, Reuters reports. The carrier said cost-cutting and stronger revenue helped it offset higher jet fuel costs. In October 2006, jetBlue announced a net loss of $500,000 for Quarter 3, and a plan to regain that loss by deferring some of their E190 deliveries and by selling 5 of their A320s.
After making a codeshare agreement with Lufthansa that went into effect in 2010, jetBlue transitioned to the Sabre reservation system used by Lufthansa, enabling the airlines to sell tickets on each other's flights, transfer luggage and passengers between the two carriers, and combine frequent flyer programs,. By making use of JetBlue's North America routes as a feeder network, the agreement put Lufthansa in a position to operate quasi-hubs in New York–JFK and Boston Logan.
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.
Also in 2010, JetBlue entered into interline booking agreements with South African Airways and American Airlines to facilitate luggage transfers between airlines for passengers with connecting flights on a different carrier. The agreement with American included JetBlue's 18 destinations not served by American and American's 12 international flights out of New York–JFK and Boston Logan. In addition, American gave JetBlue 8 round trips slots out of Washington National in D.C. and 2 out of Westchester, New York. In return, JetBlue gave American 6 round trips out of New York–JFK. The agreement with American Airlines has since ended according to JetBlue's website.