The following year, Michalak played in four of France's Six Nations fixtures all in the starting line-up. He was not used in the match against Italy. Toulouse also made it to the final of the 2003–04 Heineken Cup, though they were defeated by the London Wasps. Michalak gained four more caps in November 2004 against Argentina, Australia and the All Blacks. He played in all of France's 2005 Six Nations matches, as well as Toulouse's 2004–05 Heineken Cup victory over Stade Français. He came into the Heineken Cup final under an injury cloud, but showed no signs of it, even sealing the victory for Toulouse in the end with a late drop goal, having also scored two earlier penalties. Toulouse won 18–12 and became the first ever team to win the Cup three times. He was then capped three times in June for France; twice against the Springboks and once against Australia. Michalak was capped another four times in November, against Australia, Canada, Tonga and South Africa. He was named in France's squad for the 2007 Rugby World Cup. Within seconds of coming as a substitute on in the quarter-finals of the tournament, he made a break and then made an uncalled forward pass to Yannick Jauzion who scored a try which when converted gave France a two-point lead which they held onto to beat New Zealand, the tournament favourites. Wayne Barnes missed this call, and has been critcised heavily since.