The Agera was the first model to feature the Koenigsegg developed Vortex Generating Rims (VGR). They acted as air turbines to draw air in to improve brake cooling, and assisted with increasing the downforce of the car significantly. Given that the offset and width are different from front to rear, all four wheels are individually designed so that turbine blades always face the correct direction for extraction. The VGR wheels are forged and then machined to their final shape (excess material is removed during this process) thus minimizing weight whilst featuring outstanding stiffness.

Turbo technology had come a long way since the CCX and CCXR, with the downside of turbo lag disappearing if engineered properly. However, turbo engines with emission control had catalytic converters that caused a lot of back pressure at high power levels. This was elevated through the turbo and into the exhaust ports of the engine, causing hot EGR - a source for detonation knocking. To solve this, Koenigsegg placed the pre-cat behind the wastegate instead of the turbo, reducing back pressure by a factor of 3. This solution gave an extra 300 hp – a worthy successor of the Rocket cat invented by Christian 10 years prior. This meant that the Agera could competitively deliver torque, power and response to match larger engines at a fraction of their weight.

The Agera's 7-speed automatic gearbox was developed together with CIMA. Its primary shifting function is that of a single clutch but it has a secondary, smaller wet clutch. The benefit of this is that it acts as a single clutch box but has shift speeds of a twin-clutch box. The result is that this system is smaller, more compact and lighter than a twin-clutch box.