His tenure at the Kunstgewerbeschule under Hermann Dyck, however, was only of short duration. In the first semester he transferred to the class of Classical Art of Johann Georg Hiltensperger and Alexander Ströhuber, where the students learned about the aesthetic ideals of antiquity.

In 1865 Grützner joined the painting class of Hermann Anschütz at the Munich Academy. Meanwhile, he also sought advice and inspiration from Carl Theodor von Piloty until he was taken into his class in 1867. Piloty's class was packed with aspiring artists from around the world, from Hungary, Greece, Germany, Russia, and Poland. After three years under Piloty, Grützner left the academy.

In 1870 he moved into his own studio in the garden house of Schwanthalerstraße 18 in Munich. He quickly began to produce one painting after another. He made his career in Munich and was very successful. It was reported by artist and writer Friedrich Pecht in the journal Die Kunst für Alle (Art for All) in 1886: "the painters Eduard Grützner and Ludwig Willroider were granted the title of "professor" by Luitpold, Prince Regent of Bavaria. In 1880 he was awarded the Order of Merit of St. Michael (Knight's Cross) first class. He was knighted in 1916.

Grützner was an avid collector of art. Early on he favored pieces from the German late Gothic and early Renaissance. In the last decade of his life, he turned away from the late Middle Ages and collected art from the Far East. In his major compositions, however, he almost always included old pieces, mostly from his antique collection.

In 1874 Grützner married Barbara Link, who two years later bore him a daughter, whom they named Barbara. In 1884, after ten years of marriage, his first wife died. In 1888, he became engaged to Anna Grützner Wirthmann, the daughter of a Munich garrison commander, and a short time later their son Karl Eduard was born. This second marriage was less harmonious and eventually his wife, who was some 17 years younger, left him for a Viennese singer.

In his old age he sought solace in Chinese philosophy, and began to collect items from the far east and learn Japanese. Occasionally he included a Buddha figure or a Chinese vase in some of his paintings. He also painted a number of ascetic looking cardinals, often with harsh and unsympathetic features. He died on April 2, 1925 in Munich.

Grützner was, along with Carl Spitzweg and Franz von Defregger, one of Munich's leading genre painters in the second half of the 19th century. The paintings Grützner is best known for combine detailed academic rendering with humorous and anecdotal subject matter, often depicting monks drinking.

Grützner was one of Hitler's favorite painters, Albert Speer quoting him as saying of one of the artist's works that he was "greatly underrated... Believe me, this Grützner will someday be worth as much as a Rembrandt. Rembrandt himself couldn't have painted that better."