In 1865 appeared his monograph on Henry the Lion, duke of Saxony and Bavaria, which was followed by three volumes on the emperor Frederick Barbarossa (Kaiser Friedrich I., Danzig, 1871–1874).
In 1874 he received a government commission to undertake explorations in Syria, particularly at Tyre, and as a result be published in 1876 Aus Phönicien, a collection of historical and geographical sketches.
Then turning to a wider theme Prutz contributed to Oncken's university history the two volumes on the political history of Europe during the Middle Ages (Staatengeschichte des Abendlandes Im Mittelalter, Berlin, 1885–1887).
In 1888 he reverted to a subject which he had touched upon in his Geheimlehre und Geheimstatuten des Tempelherrenordens (Danzig, 1879), translated into English as The Secret Teaching of the Knights Templar (2015), and wrote the history of the rise and fall of the Templars (Entwickelung und Untergang des Tempelherrenordens).
[1] In 1902 Prutz resigned the chair of history in the University of Königsberg, which he had held since 1877, and took up his residence at Munich.