FIFA's developers made a complete overhaul of the game engine for this installment of the game, claiming a dramatic increase in the control of play, having rewritten more than half the game's code. In addition to a renovation of the engine, which discards the "off the ball" system, the developers boasted a significantly more involved Career mode and the introduction of "team chemistry" which determines how well team members play together. This installment breaks with the long tradition of commentary from Match of the Day's John Motson and (more recently) Ally McCoist, who are replaced by ITV's Clive Tyldesley and former Sky Sports pundit Andy Gray, who had already worked in the series as guest commentator.
One of the new features in FIFA 06 was a special "retro" which features nostalgia of the game. Inside it includes an unlockable classic biographies section, a memorable moments video compilation which features ten of the most memorable moments as judged by the FIFA 06 developers, a video compilation with a retrospective view of every game in the FIFA series and the chance to play the first ever game in the FIFA series which was titled as "FIFA 94". The game also features for the first time a Classic XI team consisting of great football legends and a World XI team consisting of current great superstars. Both teams have the Cardiff Millennium Stadium as their primary ground. These clubs must be unlocked in the "Fan Shop".