In June 2009, the squadron deployed ten jets to RAF Akrotiri, Cyprus, eight of which continued to Kandahar in Afghanistan. This marked the start of Tornado GR4 operations in Afghanistan, with the type replacing the Harrier GR9 in theatre. For over four months, No. 12 (B) Squadron successfully provided support to the International Security Assistance Force (ISAF), including close air support for, amongst others, British, American, Canadian and Afghan troops in all parts of the country. On 16 October 2009, No. 12 (B) Squadron returned to Lossiemouth after having handed over to a Marham-based GR4 squadron.