Schlüter's first known work was the decoration of the facade of the St. Johannis Chapel, or Danzig Royal Chapel, in 1681. He later created statues for King John III Sobieski's Wilanów Palace in Warsaw and sepulchral sculptures in Żółkiew (Zhovkva). In 1689, he moved to Warsaw and made the pediment reliefs and sculptural work of Krasiński Palace.
Schlüter was invited to Berlin in 1694 by Eberhard von Danckelmann to work as court sculptor at the Zeughaus for Elector Frederick III. His sculpted decorations are a masterpiece of baroque expression and pathos. While the more visible reliefs on the outside had to praise fighting, the statues of dying warriors in the interior denounced war and gave an indication of his pacifist religious beliefs (he is said to have been a Mennonite). Travelling through Italy in 1696, he studied the work of masters like Michelangelo Buonarroti und Gian Lorenzo Bernini.
Schlüter also worked as an architect and built many state buildings in Berlin in his role of "Hofbaumeister" (Court Architect), which he lost when one tower showed signs of a weak fundament. He also served as director of the Akademie der Künste from 1702 to 1704, after which he began concentrating on sculpting again, as "Hofbildhauer" (Court Sculptor). His most important equestrian sculpture is that of the "Great Elector", Frederick William of Brandenburg, cast in 1708 and placed at "Lange Brücke" near the Berlin City Palace, now situated in the Charlottenburg Palace.
The Berlin City Palace, and many of his works, were partially destroyed by bombing in World War II and by the subsequent Communist regime. A similar fate probably happened to the Amber Room, made between 1701 and 1709, Schlüter's most famous work of architecture.
In 1713 Schlüter's fame brought him to work for Tsar Peter the Great in Saint Petersburg, where he died of an illness after creating several designs. Together with Johann Friedrich Braunstein, he designed the Grand Palace and Monplaisir Palace in Peterhof. Also the city's oldest building, Kikin's Palace, and the reliefs at the Summer Palace are attributed to him.