1963 Michael Werner opened the gallery "Werner & Katz" together with Benjamin Katz in Berlin on Kurfürstendamm. The first exhibition showed works by Georg Baselitz. The exhibition was closed by the public prosecutor's office for "causing public nuisance," and the paintings "Die große Nacht im Eimer" (which now hangs in the Museum Ludwig in Cologne) and "Nackter Mann" were confiscated.
In 1964 Michael Werner opened his own gallery with the "1st Orthodox Salon" in a former coal shop on Pfalzburger Strasse in Berlin.
In 1968 he moved to Cologne and took over Galerie Hake, which he continued to run as Galerie Michael Werner from October 1969. Since that time, the gallery has successfully represented internationally some of the most important post-war German artists as well as prominent American and European artists. Artists at the gallery include Georg Baselitz, Marcel Broodthaers, James Lee Byars, Jörg Immendorff, Per Kirkeby, Eugène Leroy, Markus Lüpertz, A.R. Penck, Sigmar Polke and Don Van Vliet. The gallery also shows works by classical modern artists such as Otto Freundlich, Ernst Ludwig Kirchner, Wilhelm Lehmbruck, Henri Michaux, Francis Picabia and others.
From 1982 on, Michael Werner established artists of the gallery in the USA first through cooperation with the renowned New York galleries Ileana Sonnabend, Pace Gallery, Xavier Fourcade as well as Marian Goodman and then with Mary Boone Gallery.
In 1990, Michael Werner Gallery opened its space on New York's Upper East Side with Georg Baselitz's "Heroes" paintings.
In January 2007, under the title "Michael Werner. Une saison à Paris" in the rooms of the renowned Galerie de France, Michael Werner held a series of exhibitions with artists from the gallery.
In 2008, the Michael Werner Gallery opened an office in Berlin and took over the Julius Werner Gallery for its exhibitions, which was operated by VeneKlasen/Werner from September 2009 to July 2016.
In 2012, Michael Werner Gallery opened another location in the London Borough of Mayfair with an exhibition of new paintings by Peter Doig.
In August 2009, the Berlin office was initially relocated to Märkisch Wilmersdorf - then back to Berlin in 2021, to Hardenbergstraße 9a, Charlottenburg, initially in a temporary space on the second floor. After the closure of the Cologne location at the end of 2022, the main premises on the first floor were additionally opened in March 2023.
In 2024, Michael Werner opens new spaces in Los Angeles and Athens.