In March 2003, Hawaiian Airlines filed for Chapter 11 bankruptcy protection for the second time in its history. The airline continued its normal operations, and at the time was overdue for $4.5 million worth of payments to the pilots' pension plan. Within the company, it was suggested that the plan be terminated. As of May 2005, Hawaiian Airlines had received court approval of its reorganization plan. The company emerged from bankruptcy protection on June 2, 2005, with reduced operating costs through renegotiated contracts with its union work groups; restructured aircraft leases; and investment from RC Aviation, a unit of San Diego-based Ranch Capital, which bought a majority share in parent company Hawaiian Holdings Inc in 2004.
In March 2007, Hawaiian introduced a "tasting menu" or "tapas menu" for its first class passengers on its U.S. mainland and international flights. The menu consists of twenty entrees set on a rotation, with five available on any given flight. Passengers are provided information on the available entrees for their flight when they board, or shortly after takeoff and may choose up to three entrees as part of their inflight meal.[95][96]
In February 2018, Hawaiian was rumored to be canceling its order for six A330-800s and replacing them with 787-9s.[82] It was reported that Boeing priced the aircraft at less than $115 million, and possibly less than $100 million, each; the production cost of a 787-9 is between $80 million and $90 million. Boeing Capital also released Hawaiian from three 767-300ER leases in advance; these aircraft were to be transferred to United Airlines. Initially, Hawaiian refuted it cancelled its A330-800 order, but did not dismiss a new deal with Boeing.[83] However, on March 6, 2018, Hawaiian Airlines confirmed the cancellation of the A330-800 order and the signing of a Letter of Intent with Boeing to purchase ten 787-9 aircraft, with options for an additional ten planes;[84] the deal was finalized at the Farnborough Air Show in July 2018.[85]

On August 30, 2012, Hawaiian filed an application with the U.S. Department of Transportation for a nonstop route between Kona and Tokyo-Haneda.[41] This would fill a void that Japan Airlines left when it ceased service to Kona nearly two years earlier.[41] However, the US Department of Transportation rejected the airline's application to begin service.[42]
On February 11, 2013, the airline announced a new venture in the turboprop interisland business, "ʻOhana by Hawaiian." Service is operated by Empire Airlines using ATR 42-500 turboprop airplanes. Service began on March 11, 2014, to Molokaʻi and Lānaʻi.[44] The airline expanded more "ʻOhana by Hawaiian" routes between Kahului, Kailua-Kona & Hilo during the summer of 2014.
In October 2015, Hawaiian Airlines announced that they will be upgrading their business class seats from the standard cradle seats to a 180-degree lie-flat seats on their A330 fleet in a 2-2-2 configuration. The new seats will be installed starting the second quarter of 2016. In addition to the new business class seats upgrade, the airline will add 28 additional Extra Comfort seating.[101]