In the second quarter of 2007, the load factor was at about 79%, after about 92% in the year before. Subsequently, the company announced the closure of its Leipzig/Halle and Bremen bases, in order to grow in Cologne/Bonn instead. On 29 January 2008, plans were announced to merge TUIfly with Eurowings and Germanwings (the Lufthansa low-cost brands) into a joint and independent holding company, but were withdrawn as talks turned out to be unsuccessful.
TUI Travel confirmed on 27 March 2009 that it had sealed a strategic partnership with Air Berlin that would see Tui Travel take a 20% stake in Air Berlin, and Air Berlin 20% in TUIfly. Due to regulatory matters, this was changed to 9.9%. Air Berlin will also wet-lease 17 aircraft from TUIfly and take over all of TUIfly's city connections. TUI will focus on serving the charter market with 21 aircraft of the remaining fleet. From 25 October 2009, all German domestic flights previously operated by TUIfly were taken over by Air Berlin, as well as all flights to Austria, Italy and Croatia. Most of these flights are still operated by TUIfly aircraft, but are marketed by Air Berlin.
In December 2013 TUIfly announced to abandon their distinctive yellow livery and replace it by the new blue design already introduced at Arkefly, Jetairfly and Thomson Airways. The first plane in the new colours arrived in Hannover on 17 February 2014.
All flights within Germany and other non-tourist destinations are operated on behalf of Air Berlin and the service of Air Berlin. TUIfly offers free drinks, snacks, and meals on flights to and from Cape Verde, Egypt, Greece, Israel, southern Italy, Morocco, Portugal, Spain (including the Canary Islands), and Tunisia. Hot meals are served on the longest flights, including those to the Canary Islands, Cape Verde, Egypt, and Madeira.