[citation needed] When Balthasar's father died in 1560, his mother sent the 12-year-old youth to Fulda monastery, where her brother, Wilhelm Hartmann Klauer von und zu Wohra, was prince-abbot.
In 1570, he was elected his uncle's successor as prince-abbot and confirmed in that position by Pope Pius V. As abbot, Balthasar helped his brothers Otto, Melchior, and Wilhelm attain high office.
Whereas his predecessors had tolerated Protestantism, resulting in most of the citizenry of Fulda and a large portion of the principality's countryside professing Lutheranism, Balthasar ordered his subjects either to return to the Catholic faith or leave his territories.
In 1576, the combined opposition forced Balthasar at Hammelburg to sign a letter of abdication and made Julius Echter administrator on the condition that he would tolerate the knights' religion.
The Pope threatened Julius Echter von Mespelbrunn with excommunication if he refused to relinquish his claim to Fulda, but the latter insisted on the matter being settled by lawsuit, which would last more than a quarter century.