[6] Subsequently, TransNusa agreed to further co-operative partnerships in Nusa Tenggara with Riau Airlines using Fokker 50s with a second Trigana supplied ATR 42 introduced in April 2006.

[8]By March 2008, TransNusa was operating 4 Fokker 50 turboprop aircraft in fleet co-operation arrangements with Riau Airlines.

On 10 September 2008, Mandala Airlines announced arrangements with TransNusa to supply further feeder services from Jakarta via Surabaya providing services to passengers through the Kupang hub, connecting to and from destinations including Ende, Sika, Bajawa, Lombok, Waingapu, Tambolaka, Labuan Bajo and Alor.

The co-operation with IAT grew the airline's ATR 42-300 fleet to four aircraft by the end of the year[12][13] In 2010, TransNusa offered connections into the Sriwijaya Air network to link directly with flights from Kupang to Surabaya and Jakarta.

Impacted by the effects on the industry by the COVID-19 pandemic, the airline suspended operations in September 2020, which led to its fleet being transferred back to lessors.

[16] In November 2021, TransNusa announced through Instagram that the airline intends to return operating, although as a low-cost carrier in place of its former regional model.

Pre-purchase of meals is available at a lower price than on board, and with additional options As of January 2025[update], the TransNusa fleet consists of the following aircraft.