Spain’s continuing sovereignty dispute with the United Kingdom over the territory where the airport stands (different from the generic one on Gibraltar itself) has seriously affected the airport’s operations. In December 2, 1987, an agreement was signed between the governments of the United Kingdom and Spain to allow the joint civil use of the airport The agreement foresaw the building of a new terminal in the neighbouring Spanish municipality of La Línea de la Concepción adjacent to the northern side of the existing frontier. However, the agreement was blocked by the Government of Gibraltar, led from 1988 by Joe Bossano. As a result, the agreement was never implemented.
Since then, Spain successfully excluded Gibraltar from European wide de-regulation initiatives, preventing direct links from Gibraltar to the rest of the European Union (except the United Kingdom), on the grounds that no regulation that somehow recognises the sovereignty of the United Kingdom over the isthmus may be implemented without a previous agreement on the airport.
By late 2005 and early 2006, the implementation of a new agreement was one of the main topics of the Gibraltar Trilateral Forum being held between the Governments of Gibraltar, Spain and the United Kingdom. As a result, the Córdoba Accord was signed on 18 September 2006 by all parties. This ended all discriminatory restrictions on civilian flights to Gibraltar Airport, including the prohibition of flights over Spanish soil, and exclusion of Gibraltar from all EU agreements on air transport, allowing civilian flights from all nations into Gibraltar Airport.
On 17 November 2006 Iberia announced that it would start flights from Madrid to Gibraltar using Airbus A319 aircraft. This was a landmark move as no Spanish airline had flown to Gibraltar since 1979, because of its disputed status.
Iberia began flights to Gibraltar Airport on 16 December 2006 with a flight from Madrid that included some members of the Spanish Government on board. GB Airways flew a one-off flight in the other direction with a group of children from the Gibraltar area making up the passengers. In May 2007 GB Airways (flying as a British Airways franchisee) also began operating the route between Madrid and Gibraltar, however, this was discontinued on 30 September (leaving Iberia to work the route alone).
On 12 September 2008 Monarch Airlines resumed services from Gibraltar to Manchester Airport three times a week every Monday, Wednesday and Friday. No other airline has operated services from Manchester into Gibraltar since Monarch withdrew the route in July 2006. Currently, the route is operating on a Sunday as well until 31 October, and will also operate on a Thursday in the summer season next year.
On 22 September 2008 Iberia announced that it would cease its flights to Madrid by 28 September due to "economic reasons", namely, lack of demand. This left Gibraltar, once again, without any air links with Spain.
In April 2009 Ándalus Líneas Aéreas restored Gibraltar's airlinks with the Spanish capital. In July 2009 Ándalus also began scheduled flights to Barcelona, increasing the destinations in Spain to two. However, the airline ceased to serve this route in September 2009 due to a lack of demand. In April 2010 it was confirmed that Ándalus flights to and from Gibraltar had been indefinitely suspended. And now yet again, Gibraltar has no direct air links to Spain. Ándalus Líneas Aéreas ceased operations on 13 August 2010.