In 1989, Ford resources began to focus on the next Mustang, due to debut in late 1993.^[9] There would be few changes in the model line through its retirement in 1993. Most changes would be visual. For 1990, a limited run of 4,103 emerald green exterior, and white leather interior 5.0 LX convertibles, and a limited run of 5,897 silver exterior, and grey interior 5.0 GT hatchbacks were produced for a contest held by 7-Up, but the contest was cancelled at the last second. Similarly, for 1992 and 1993, three special-edition 5.0 LX convertibles were released in the spring. These models had with Vibrant Red exteriors with Oxford white leather interiors for 1992, Canary Yellow exterior with black or white leather interior, or Vibrant white exterior with white leather interior, for 1993.

The 1991 model year changes to the 2.3 L I4 engines included an increase in horsepower (from 88 to 105) due to a revised cylinder head with two spark plugs per cylinder.

With the end of the run near in 1992, Ford switched to cast hypereutectic pistons for all 302 cu in (4.9 L) engines and also re-rated the 5.0 GT to 205 hp (153 kW) and 275 ft·lbf (373 N·m) of torque. This estimate was more accurate given the previous power ratings were made before the addition of the mass air flow system, minor revisions in the camshaft profile, and other various small changes made throughout the production run.

Under the newly established Ford SVT division, the 1993 Ford Mustang SVT Cobra was offered with the 302 cu in (4.9 L) V8 that produced 235 hp (175 kW) and 280 ft·lbf (380 N·m) of torque. Featuring more subdued styling than the GT, the Cobra used Ford's new GT-40 high-performance engine equipment, which could send a Mustang through the ¹⁄₄ mile (0.40 km) in low 14 seconds. A Cobra R model was also produced for 1993 that used the same engine as the regular Cobra. It featured larger brakes, Koni shocks and struts, an engine oil cooler, a power steering cooler, and a factory rear seat delete. Since the Cobra R was race oriented, options such as air conditioning and a stereo system were not offered. Production of the third generation Mustang concluded in September 1993. 1993 was also the first year that a CD player was offered from the factory.