The third generation, B6 platform S4 debuted in mid-2003. Despite having motivated to yet another completely new platform, the S4′s most publicized new quality was its engine. It became available in three body styles for the 2004 model year: the S4 sedan, the S4 Avant wagon and a convertible, the Audi S4 Cabriolet.

Changing the 2.7 L bi-turbo V6 engine of the old generation S4 was a 4.2 L, 40-valve V8 based on the unit from the A8 and producing 344 PS (253 kW/340 hp), making it more potent than both the S6 Plus, or RS2 and nearly as powerful as the B5 platform RS4. With such abundant power on tap, the B6 S4 could accelerate swiftly enough to meet or beat the times of most sports cars. Road experiments conducted by American automotive magazines indicated that it could go from a standstill to 100 km/h in 5.2 seconds, and make it to 200 km/h (124 mph) in slightly over 20 seconds, although doing this lead to fuel use dipping into single digits, considerably lower than the earlier models, leading to the addition of a gas guzzler tax in North America.

Like its predecessors, the modle was standard with a six-speed manual and Quattro, the Tiptronic transmission remained an opportunity. The B6 platform S4 was traded by the B7 platform S4 in late-2005. Enthusiast progress on the V8 engine used in third and fourth generation S4 has lagged. None of the available modifications have made this car faster than the modified S-cars of previous generations, although the long discussed, intangible, supercharger kits may alter this situation.
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