In February 2006, afterward England captain Michael Vaughan and vice-captain Marcus Trescothick acceptable bare for the aboriginal Test bout adjoin India, Flintoff was called captain of the England aggregation and after appear that he would be blockage in India for the absolute Test series, although he and his wife were assured their additional child. His wife gave bearing to a son, Corey, anon afore the additional Test on 9 March.
On the field, Flintoff was apparent as a abundant success during the fatigued alternation with India, with a 212-run achievement in Mumbai. His contributions with both bat and brawl ensured that he was called as the amateur of the series, with abounding commentators seeing Flintoff as addition who not alone formed more good beneath the albatross but was additionally beheld as a abundant access of an amateur side, which included abounding debutants, such as Alastair Cook, Owais Shah and Monty Panesar. Flintoff accumulated four fifties in the series, and took 11 wickets, on acrimonious surfaces for seamers. Flintoff connected to captain England during the seven ODIs in India, although he was adequate for two matches.
However, afterward a ceremony of his abiding abate botheration in May 2006, he absent both the ODI alternation adjoin Sri Lanka, and the aboriginal Test adjoin Pakistan. It was after appear in July that Flintoff's rehabiltation had not been acceptable to annihilate the injury, and that added anaplasty would be required. He was appropriately disqualified out for the absolute alternation adjoin Pakistan. Despite abrasion concerns, Flintoff was after called for the ICC Champions Trophy, area he played as a specialist batsman, not as an all-rounder.