In January 2009, following England's losses in India, the media reported that Pietersen had asked the England and Wales Cricket Board (ECB) to hold emergency meetings to discuss Moores' coaching role with the team. Days later, Pietersen made remarks to the media about there being an 'unhealthy situation' that needed to be resolved in the England camp. The media speculated that Moores would shortly be replaced if there was a Pietersen–Moores rift. Moores and Pietersen were believed to be in disagreement on several issues, including the team's training regimen, and the possible selection of former England captain Michael Vaughan for the upcoming tour of the West Indies. On 7 January 2009, Moores was removed as England's coach by the ECB, and Pietersen unexpectedly resigned as captain. In the immediate aftermath of Pietersen's resignation, several commentators connected with English cricket indicated that they believed that Pietersen had miscalculated by openly advocating for the removal of Moores, particularly in making their dispute public. In an interview several days after his resignation, Pietersen revealed that he had not intended to resign as captain, but was told by ECB officials that he was resigning. Dennis Amiss, the vice-chairman of the ECB, went on record backing up Pietersen in his statement that the story of the rift with Moores had not been leaked to the media by him, saying, "We don't believe Kevin Pietersen leaked the information, we understand his frustration at it being leaked by other parties." Pietersen was captain for three Test matches, and 10 One Day International matches. It was announced that Andrew Strauss would take over the captaincy.
In February 2009, Royal Challengers Bangalore of the Indian Premier League bought Pietersen for US$1,550,000, which made him the highest-paid IPL player along with Andrew Flintoff. The following month RCB owner Vijay Mallya announced that Pietersen would succeed Rahul Dravid as captain. He won two out of his six matches in charge before leaving to fulfil his international commitments with England; Anil Kumble took over the captaincy and led the Bangalore team to the IPL final. Kevin Pietersen was later bought by Deccan Chargers for the 2011 season and was sold to Delhi Daredevils in the 2012 season without having played a single game for the Chargers.
Pietersen began 2009 with questions over his form, where many pundits viewed him to be in a slump. He was dismissed first ball in the first Test against the touring West Indies side dismissed by the full, swinging ball (a delivery which he seemed to struggle against), but in the second Test made a quick 49 before falling to an attacking shot. He then suffered what seemed only a minor right Achilles injury and was subsequently ruled out of the ODI series, which England also won. In June 2009, Pietersen played in England's World Twenty20 warm-up match against Scotland, registering an unbeaten 53 in a six-wicket England victory. He also appeared in the news after accidentally hitting a 15-year-old school boy with a cricket ball from a straight-drive after the boy had bowled to him. Pietersen left the boy, from Suffolk, with a signed bat as compensation.
Pietersen joined the England Ashes squad in June 2009 for the upcoming 2009 Ashes series. Despite failing to surpass single figure scores during a warm-up match against Warwickshire, he helped England to a score over 400 on 8 July during the first day of the first Test at the SWALEC Stadium, Cardiff with 69 before being dismissed by Nathan Hauritz, top-edging a sweep to a ball outside off stump; the dismissal was heavily criticised. He also seemed to flare up his Achilles injury again suddenly which hampered his batting a bit. In the second innings he was bowled for 8 after leaving a straight ball from Ben Hilfenhaus. Many pundits thought the criticism of England's key batsman from the first innings possibly affected him. In the first innings at Lords, after proving his fitness, he came at 222–2 and played some trademark shots before being caught behind off Peter Siddle. In the second innings he came in when England had a lead of almost 300 and he and Ravi Bopara batted for time. Pietersen limped when he ran and many shots ran off the inside edge which raised serious doubts for the rest of the series. He actually did well to reach 44 before being caught behind off Siddle again. After struggling in the field as England won, Pietersen was ruled out of the rest of the series with an Achilles injury. This brought to an end 54 consecutive Test matches. As his recovery slowed, Pietersen was not included in the 2009 ICC Champions Trophy and Andy Flower speculated that due to an infection of the wound Pietersen "may miss this winter's tour of South Africa because of slow progress in recovery from surgery."