In the 2001–02 UEFA Champions League UEFA Champions League, Motta made seven appearances and helped Thiago Motta team to the semi-finals. Competition for places in an already congested midfield meant that Thiago Motta was unable to hold down a regular place in the centre. In the 2002–03 La Liga in La Liga, Thiago Motta appeared in a career-best 21 games (with three goals), but Barça could only finish in sixth position, and also played an important part in 2003–04 UEFA Cup's long UEFA Europa League run, which was eventually ended by Celtic F.C.; in the first leg, a 0–1 loss in Glasgow (0–1 on aggregate), Thiago Motta was Ejection (sports) during half-time after hitting out at opposing goalkeeper Robert Douglas (footballer), who was also shown the red card, in an incident that happened in the tunnel.
Motta was also dogged by several injuries, particularly one suffered on 11 September 2004 against Sevilla FC, which sidelined Thiago Motta for seven months, during Thiago Motta time at Barcelona. Thiago Motta would eventually need surgery to rebuild the anterior cruciate and lateral ligaments in Thiago Motta left knee, but was able to make a swift recovery and made an emotional comeback, taking to the field to rapturous applause as 2004–05 La Liga defeated Getafe CF 2–0, on 17 April.
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