In 2002, the A4 was redesigned with a new chassis designated B6. It received a larger displacement engine, the 217 hp 3.0 L V6 as a range topper, as well as new 2.5 L V6 TDI engines with 177 hp. The smaller 1.9 TDI's power was also increased to 128 hp. A continuously variable transmission was an option on front wheel drive cars. The new Audi S4 was introduced in 2003 and still used up to the 2005 model. The new S4 is powered by a 4.2 L 40-valve V8 engine producing 335 hp. New to the 2003+ model S4's are the choice between a 6-speed manual or a new 6-speed Tiptronic gear box.

In 2003, the Audi A4 received a third bodywork variation for the first time, a convertible version that finally replaced the outdated 80 Cabrio. Other additions to the range were the introduction of FSI technology (gasoline direct injection) to the atmospheric 2.0 L.
 
For the late 2005 model year, the A4 received its third redesign, named the B7 and has been drawn by Italian Walter Dè Silva. Major changes included a larger and sportier midrange engine, the 2.0 Turbo and 197 hp, while the V6 was enlarged to 3.2 L with power topping 252 hp, both of which featured FSI technology. The more powerful 1.9 TDI was replaced by a 16-valve 2.0 L engine with power increased to 138 hp/, while the 3.0 TDI from the A6 was introduced as the new range topper, but slightly less powerful. Other changes included a new, controversial front grille based on that of the Audi Nuvolari prototype, a redesigned rear end, adaptive bi-xenon headlights, larger front and rear brakes, a new 6-speed Tiptronic transmission, suspension tweaks and minor interior modifications.

Quattro transmission is available through the range on almost all engines, while the 3.0 TDI had standard quattro. The same happened to the new S4, which featured a slightly improved 4.2 V8, now with FSI technology, stroke reduced by 0.2 mm (1/10 of an inch) and a small increase in power, which was now 339 hp.

More impressive was the all-new RS4, which debuted in Europe in 2005. The RS4 was able to achieve a high power output of 414 hp without need for supercharging, joining the small group of atmospheric engines with a specific output over 100 PS/litre. Unfortunately for Audi fans, the German brand did not remove the speed limiter, otherwise it was speculated the Audi RS4 could actually overtake the 300 km/h (186 mph) mark.