Count Rudolf, a partisan of the future Emperor Frederick I Barbarossa, was able to expand his family's possessions and they eventually owned fiefs from the Danube to the Grisons.

However, the prince-bishops of Constance, as the biggest landowners in the Linzgau and patrons of several religious institutions such as Holy Spirit Hospital in Pfullendorf, continued to exert significant political influence over the whole area.

At the Council of Constance (1415), King Sigismund granted Blutgerichtsbarkeit ("Blood justice" or the right to pronounce sentences of death or mutilation) to the town, a status that confirmed the city as being answerable to God and to the Emperor only.

During the administrative reforms that occurred from 1972 to 1976, the neighboring villages of Aach-Linz, Denkingen, Gaisweiler, Tautenbronn, Großstadelhofen, Mottschieß, Otterswang, and Zell-Schwäblishausen became part of Pfullendorf.

In 2001 the United States Army took command of the I-LRRP School in Pfullendorf and the name was changed to the International Special Training Centre (ISTC).