The airline changed affiliations to Continental Airlines in December 2000, when US Airways did not renew the codeshare agreement. In July 2001 the company announced plans to downsize its fleet and workforce by approximately half and begin a reorganization of the airline. In early 2002 the company began a "micro-hub" operation based in Albany, New York. At its high point in 2003 and 2004 the hub served the following cities: Allentown, Harrisburg, Buffalo, Rochester, Syracuse, Burlington, Manchester, Portland, Bangor, Providence, Islip, Hartford/Springfield, White Plains, Ottawa and Montreal, all with a fleet of Raytheon Beech 1900Ds. Service was also provided out Boston's Logan International Airport to Rutland, White Plains, Allentown, Burlington, Wilkes-Barre/Scranton, Islip, Saranac Lake, and Plattsburgh. Following unprofitable operations as Continental's regional affiliate in Albany and Boston, all operations were gradually shifted towards the midwest in 2005.

In January 2003, CommutAir announced an agreement with Continental to feed the latter's Cleveland, Ohio hub. Service was commenced on March 16, 2003 with service to Kalamazoo, Michigan and Elmira, New York. Two cities were added the following month and by August 2003, CommutAir served 12 cities from the Cleveland hub. As of May 2007 the company has expressed plans to move operations from Plattsburgh to the Cleveland area, according to News Channel 5, WPTZ.

On May 20, 2008, Commutair's pilot group voted, 107 out of 118 eligible voters, for union representation by the Air Line Pilots Association.