In 1989, halfway through its expected build life, the FC RX-7 saw a multitude of small refinements. Rotary engine technology had had continued its advance in the 3 years. The engines themselves used new lighter, higher compression rotors. The combustion recesses on the rotors were fully machined and chromed for heat control. With the machining, the compression ratios of each of the rotor's combustion chambers as well as rotor weight, could be more closely matched. The side seal thickness was reduced from 1.0 mm to 0.7 mm. The compression ratio jumped to 9.0 for the turbo (up from 8.5). For increased emission restrictions and better engine management the engine computer was speed was doubled.

The airflow meter was also changed from the flapper type to a linear type for reduced air resistance and more precise measurement. The oil metering pump was changed from a mechanical pump to an electronic model for more effective lubrication and reduced oil consumption.

The Turbo II received a new turbocharger. Mazda called it the "Completely Independent Twin Scroll". The impeller was fed directly at the exhaust port. The Mazda press release in 1989 said: “This permits the powerful exhaust pulse generated by the opening of the exhaust port to directly hit the turbine blades without interference from the exhaust from the other rotor." This newer design resulted in reduced turbo lag and increased torque. The new electronically controlled wastegate allowed higher boost pressures and quicker response. The modifications resulted in the peak torque smoothed through the 2000 to 5000 RPM band. The horsepower also climbed another 18 ponies to give the revised Turbo II a Mazda claimed total of 200 horse power @ 6500 RPM and 196 lb-ft of torque at 3500 RPM.