In April 1999 Swissair bought a 20% minority stake in TAP after the portuguese government tries to privatise the Airline. Following this, TAP enters the Qualiflyer Alliance and joined the Qualiflyer FFP gicing up their own FFP 'Programa Passageiro Frequente'. As a QG member many codeshare flights with other QG Partners are introduced, most noticeably also with Portugalia, the other large portuguese carrier, which is also part of the QG. Within the Qualiflyer GRoup TAP is the stronghold to Brazil, introducing further flights to the South American country. After Swissair went bankrupt after the 9/11 attacks, TAP and the Qualiflyer Group are weakened and on February 13, 2002 all Qualiflyer Alliance joint activities were discontinued except for the Qualiflyer frequent flyer program, which was later also discontinued and transformed into the 'TAP Navigator' Programme.

Following these and other changes TAP was finally in recovery mode and on its way back to profits. Thus, the company starts new flights to further brazilian and european destinations, flying to around 40 destinations in 25 countries, and is one of Portugal's top ten employers.

On February 1st, 2005 the company introduced a new corporate identy and new liveries for their aircraft. The first aircraft to wear the new colors is Airbus A310 CS-TEX. The Name changes from 'TAP Air Portugal' to just 'TAP Portugal'.

On March 14th, 2005 TAP officially joined the STAR Alliance as a full member. Further flights to Brazil are introduced following the demise of the brazilian flag carrier (and also STAR Member) Varig.

At the same time, the Frequent Flyer programme changes its name again and is now TAP Victoria, and allowing passengers to collect miles and all STAR Airlines.

On June 18th, 2007 TAP buys its fomer competitor PGA and the company is fully integrated into TAP, buth with the Marketing name 'PGA' still being used.