The third year of production, 1969, brought several new additions to the Cougar lineup. A convertible model was now available in either standard or XR-7 trim. These highly anticipated soft tops proved quite popular and today are considered, by many, among the most desirable of the '67-'70 production run. On the exterior, the grille switched from vertical bars to horizontal bars, and a spoiler and a Ram Air induction hood scoop were added as options. A new performance package appeared and several disappeared. The XR-7G and the 7.0-L GT-E disappeared, but the 390 and 428 V8s remained. The 290 hp (216 kW) 351 Windsor V8 was added to the engine lineup. The Eliminator performance package appeared for the first time. A 351-in3 four-barrel V8 was standard under the hood, with the 390 four-barrel V8, the 428CJ and the Boss 302 available as options. The Eliminator was the new top-of-the-line performance model of the Cougar lineup. It also featured a blacked-out grille, special side stripes, front and rear spoilers, an optional Ram Air induction system, and a more performance-tuned suspension and handling package. It also came in a variety of vibrant colors, such as White, Bright Blue Metallic, Competition Orange, and Bright Yellow. Only two Cougars came with the Boss 429 V8, making them the rarest Cougars ever built. Both were factory drag cars built for "Fast Eddie" Schartman and "Dyno" Don Nicholson.

Only a limited number of Eliminators were produced: 2,250 cars in total.