Keane was involved in further controversy in the wake of Ireland's defeat by France in the qualification 2010 World Cup play-off. During an Ipswich Town press conference on 20 November 2009, Keane was critical of the Irish reaction to the Thierry Henry handball incident. His response included criticisms of the Irish team's defence and the FAI authorities.
In an interview with The Irish Times on 21 February 2009, Keane cited differences with Sunderland 30% shareholder Ellis Short and strains with club chairman Niall Quinn as the factors in his decision to resign as Sunderland manager.
On 23 April 2009, Keane was appointed as the new manager of Ipswich Town on a two-year contract, the day after the club had dismissed Jim Magilton. His first game in charge came the following Saturday with a 3–0 away win over Cardiff City, the final league match to be played at Ninian Park. The following week, Ipswich rounded off the season with a 2–1 win over Coventry City. In the 2009–10 season, Keane started to sign some players, some of them from his former club Sunderland. He signed goalkeeper Márton Fülöp, midfielders Carlos Edwards and Grant Leadbitter and brought in Jack Colback, David Healy and Daryl Murphy on loan to the club. Ipswich started without a win in their first 14 matches, making them the last team to record their first win in the whole league, finally winning on 31 October against Derby County and recording their first away win of the season on 29 November against Cardiff City. Their form gradually improved throughout the season, but Ipswich drew far too many games to come anywhere near the promotion race and they finished the season in 15th place. Many inconsistencies in the 2009–10 and the 2010–11 season meant that Keane's Ipswich side never really challenged for promotions and as a result of a poor run of form, ending up with his side dropping to as low as 21st in the Championship. Keane was dismissed as Ipswich manager on 7 January 2011.
On 6 June 2009, it was announced that Keane and his family would purchase a house in the Ipswich area, near to the training ground of Keane's new club, Ipswich Town. He eventually settled in the nearby market town of Woodbridge. They moved out of the property and offered it for sale in 2015.
In later life, Triggs was involved in a police investigation when her behaviour caused an argument between Keane and a neighbour. She appeared in an Irish Guide Dogs advertisement in 2009 – whereupon the Irish Examiner referred to her as "football's biggest canine celebrity" - and also received her own profile on Facebook. Triggs was described as a "celebrity" and a "household name" upon erroneous reports of her death from cancer in September 2010. Keane was described as "inconsolable". The Irish Examiner's obituary noted how "At critical moments when the nation's happiness seemed entwined with Roy's moods, he turned to his Labrador Triggs and took to the road".