Another major restyling took place for the 1969 production year.

Most notably, the familiar sculptured sides that had been present since the debut of the Mustang were gone, replaced with a raised body line running along the upper side from the headlamp to the quarter panel. In front of the rear wheels on coupe and convertible models is a simulated air exhaust vent. On the fastback model, now called the SportsRoof, a non-functional air scoop was added to the quarter panel directly behind the door handle. A four-headlamp design was adopted and the newly added high beam lamps were placed at the outer edges of the new plastic grille with an offset running horse and bars emblem.

On the inside, a new dash design placed four gauges, two small gauges (ammeter and oil pressure) on either side of two larger gauges (speedometer and fuel/temperature) centered behind the steering wheel. The dash pad protruded out over the instrument panel and was formed in such a way as to give the impression of a “cockpit”. New items were optional high-back bucket seats and optional headrests for the low-back buckets.

Two new engine options were added, the 351ci two-barrel and 351ci four-barrel. The 302ci four-barrel was dropped.

1969 was the last year of the GT equipment group, offering basically the same package as in 1968. Three new specialty models were developed on the SportsRoof: Mach 1, Boss 302 and Boss 429.

The Mach 1 featured a deluxe interior, high-back bucket seats, special carpet and any of the eight-cylinder engines. The hood was painted completely black and bold Mach 1 side stripes were applied.

The Boss 302 came with a modified 302ci engine, a C-shaped stripe with Boss 302 lettering, a functional front spoiler and blacked-out hood, rear deck and back panel.

The Boss 429 required special front spring towers to accommodate the big engine. It also came with a functional hood scoop and a Boss 429 decal on the front fenders. The SportsRoof simulated side air scoops were deleted on the Boss models.

Another specialty model introduced this year was the Grande, a luxury model coupe. The Grande offered a deluxe interior with wood grain trim, deluxe three-spoke steering wheel, special door panels, padded interior quarter panels and special cloth insert bucket seats. Outside were wire wheel covers, dual mirrors, C-pillar logo, duo-tone stripe under the fender line and chrome moldings around the wheel wells.

Shelby models carried an all-fiberglass front end that was very similar in design to the 1971 Mustang. A unique and controversial exhaust system was used that exited at the center rear of the car directly below the fuel tank filler.