The Mooney Mite established some of the design concepts that are still used by Mooney today. The model Mooney M20 entered production in 1955 and outwardly looked like a scaled-up Mite. Mooney is still producing variants of the M20 today.

In 1953, before funds were put in place for production of the M20, Mooney's financial backer, Charles Yankey, died of a stroke. In 1955 Albert Mooney sold his stock in the company to Harold Rachal and Norman Hoffman then left the company to work for Lockheed Corporation. Shortly after, Arthur left Mooney to work for Lockheed too.

In 1965 the company became the U.S. distributor for Mitsubishi aircraft and began selling Mooney Mu-2 operating as Mooney-Mitsubishi Aircraft Inc. In 1967 Mooney acquired production rights to the Ercoupe from Alon Aircraft Company and produced a slightly updated version as the Mooney M10 Cadet. The M10 became the final Ercoupe variant, and production ended in 1970.

Mooney went bankrupt again in early 1969 and was sold to American Electronics Labs then to Butler Aviation, which ended operations in 1971. For about three years Mooney failed to produce any aircraft. In 1973 Republic Steel Corporation acquired the rights and tooling for Mooney and resumed production in 1974. The company continued aggressive product development, working on yet another pressurized single-engine aircraft to compete with the Cessna 210. The turboprop Mooney "301" eventually became the TBM700 and is now produced by Socata Aircraft.

In 1984 Mooney merged with the French distribution firm Alexander Couvelaire. In July 2001 Mooney was the victim of yet another bankruptcy and the company was acquired by Advanced Aerodynamics and Structures, Inc. (AASI) in 2002. AASI resurrected Mooney under the name Mooney Aircraft Company, Inc.; a division of Mooney Aerospace Group, Ltd.

In 2004, MASG (AASI) sold off the Mooney assets to Allen Holding Finance in May, and filed for bankruptcy on June 10. In December 2004, MASG restructured and reacquired MAC (Mooney Aircraft Company) back from Allen Holding Finance. AvWeb has the complete story.

In November, 2004, Gretchen Jahn joined Mooney to become the first female CEO of an aircraft manufacturer. She served for about two years as a turnaround specialist. She succeeded in rebuilding Mooney's sales and dealer network. She also oversaw the development and introduction of the M20TN Acclaim and the new all-glass Garmin G1000-equipped Ovation2 GX and Bravo GX. Mooney now has a waiting list of a few months to accept delivery of a new airplane. In June, 2005, Mooney added a second shift and 50 new workers to boost production

On April 4, 2006, Mooney Airplane Company announced the release of their all-new M20TN Acclaim at the 2006 Sun 'N Fun fly-in at Lakeland, Florida. The M20TN also features the Garmin G1000 Avionics Display Suite, four heated and leather-wrapped captains chairs with lumbar support, a range in excess of 1,650 nm (400 miles greater than the Bravo GX), and a top speed of 242 knots (448 km/h) which is also 30 knots (56 km/h) faster than the Ovation 2. The Acclaim is the fastest single-engine piston-powered production aircraft in the world.

Mooney was a publicly traded company after emerging from bankruptcy under symbol MNYG (OTC BB) until October, 2006 when Mooney Aerospace Group arranged financing to buy out public shareholders.

In the fall 2007 Mooney announced the arrival of its newest model, the M20TN Acclaim Type S. The Acclaim Type S adds 5 knots (9.3 km/h) to the Acclaim's top speed, up to 242 knots (448 km/h). Mooney achieved this performance gain through aerodynamic tweaks to the Acclaim's airframe.

2008 Production Halt
On Monday 16 June 2008 Mooney announced that it would lay off 60 employees and cut production from eight aircraft per month to five. in December 2008 the company let go an additional 40 workers leaving only about 50 employees at work. The company had 25 unsold aircraft at its factory in December 2008