On 22 August 2008, Celtic announced the signing of Maloney on a four-year deal for a fee of £3 million. Maloney marked his return with a Man of the Match performance and two assists in his first match, after coming off the bench for Jan Vennegoor of Hesselink in a 3–0 victory over Falkirk at Celtic Park. Maloney scored his first goal after his return to Celtic in a 4–2 away win over Motherwell and managed his second the following week in a 3–1 away win at Kilmarnock. He finished the season with five goals, taking his total Celtic goals tally to 42.
Under new manager Tony Mowbray, Maloney played in 17 of Celtic’s first 18 fixtures of season 2009–10. However he began having trouble with his Achilles tendon after the 2–1 defeat against Rangers on 4 October 2009. Maloney played a further four games after that, but was substituted at half-time in Celtic’s League Cup defeat against Hearts. It was revealed he was suffering from Achilles tendinitis, and he did not player another game that season.
Maloney started the 2010–11 season in good form with goals against St Mirren, Hearts and a brace against Hamilton. After this run of form, Maloney was given the short-term captaincy of Celtic in the absence of Scott Brown through injury. However, fitness problems flared up again for Maloney in November 2010 when he injured his ankle during a league match against Inverness CT. He required to undergo ankle surgery in December, and didn’t return to the first team until April 2011. Maloney featured in eight of Celtic’s remaining matches; scoring against Aberdeen in the Scottish Cup semi-final and then against Motherwell in the last league fixture of the season.