In 1562 he became the court portraitist to Maximilian II. at the Habsburg court in Vienna, and later, to his son Rudolf II., both of whom seem to have much liked Arcimboldo's extraordinary portraits.

He was also the court decorator, costume designer, and general art expert. His style of early pre-surrealist portraiture was much copied by his contemporaries, making it difficult at times to differentiate his work from that of imitators.

His paintings are in Vienna's Kunsthistorisches Museum (Vienna) and in the Habsburg Schloss Amras in Innsbruck. In Italy, his work is in Cremona , Brescia , and the Uffizi Gallery in Florence. The Wadsworth Atheneum in Hartford, Connecticut , also contains pieces of his work.