The museum building was severely damaged by bombing in World War II but was reconstructed and reopened to the public on 7 June 1957, with President Theodor Heuss attending.

The new color scheme of green and red draws on the design of the rooms dating back to the time of construction of the Alte Pinakothek, and was predominant until the 20th century.

Already for King Ludwig I and his architect Leo von Klenze, the use of a wall covering alternately in red and green represented the continuation of a tradition that dates back to the exhibition of the old masters of the late 16th century in many of the major art galleries of Europe (Florence, London, Madrid, St. Petersburg, Paris, Vienna).

The Wittelsbach collection was begun by Duke Wilhelm IV (1508–1550) who ordered important contemporary painters to create several history paintings, including The Battle of Alexander at Issus of Albrecht Altdorfer.

He ordered from Peter Paul Rubens The Big Last Judgment and received Raphael's Canigiani Holy Family as a dowry of his wife.

After the reunion of Bavaria and the Electorate of the Palatinate in 1777, the galleries of Mannheim, Düsseldorf and Zweibrücken were moved to Munich, in part to protect the collections during the wars which followed the French revolution.

When the Prussians captured the Château de Saint-Cloud in 1814 as part of the War of the Sixth Coalition, they supposedly found the painting hanging in Napoleon's bathroom.

In April 1988, the serial vandal Hans-Joachim Bohlmann splashed acid on three paintings by Albrecht Dürer, namely Lamentation for Christ, Paumgartner Altar and Mater Dolarosa[10] inflicting damage estimated at 35 million euros.

[11] On 5 August 2014, the museum rejected a request by a descendant of the banker Carl Hagen for the repatriation of Jacob Ochtervelt's Das Zitronenscheibchen (The Lemon Slice) on the grounds that it had been unlawfully acquired as a result of Nazi persecution.

An investigation by the museum established that it had been lawfully purchased at the time for a fair price and that the Hagen family's interest extended only to a security on the painting.