Aurélio played a key part in Liverpool's squad during his first season, notably providing two assists for Peter Crouch and Daniel Agger in a 4–1 win over fellow title contenders Arsenal on 31 March 2007. However, Aurelio soon suffered a setback as he injured his achilles tendon on 3 April in a UEFA Champions League first leg tie against PSV. Aurélio missed the rest of Liverpool's 2006–07 campaign and returned to the squad the following season on 18 September, coming on as a substitute in a 1–1 draw against F.C. Porto in the Champions League group phase.

AurГ©lio scored his first goal for Liverpool on 2 March 2008 in a league match win against Bolton Wanderers at the Reebok Stadium. The final score was 3-1, with Aurelio scoring Liverpool's third with a volley from Xabi Alonso's corner. He then scored on the 7th of February 2009 against Portsmouth at Fratton Park with an in-direct free kick into the bottom corner, getting his team back on level terms. The final score was 3-2 to Liverpool.

AurГ©lio went on to establish himself as Liverpool's first choice left-back but was again beset with injury in the team's 1-1 draw with Chelsea in a Champions League semi-final first leg clash. AurГ©lio tore his adductor muscle after a forceful impact with Joe Cole and as a result, was ruled out for the rest of the season.

For the 2008-09 season, AurГ©lio has been in direct competition with new signing Andrea Dossena. On 14 March 2009, AurГ©lio scored Liverpool's 3rd goal with a free-kick as Liverpool won 4-1 against Manchester United, at Old Trafford. On 14 April, he scored Liverpool's opening goal in the second leg of the Champions League quarter final against Chelsea with a low curling free kick. The match ended a 4-4 draw, with Chelsea progressing to the next round on aggregate.

It was reported on Thursday July 9 that Aurelio suffered a knee injury while playing football with his children. Rumours were circulating that he would be out for 6 months but current manager Rafael BenГ­tez quashed these rumours by confirming that he would only be out for 1-2 months.