Upon returning to East Friesland in 1579 he took the position of rector in the very school in which he was taught, the college at Norden. He was subsequently sacked by the local court in 1587 because, as a Calvinist, he would not subscribe to the confession of Augsburg. Following this, in 1588, the Calvinist count Johan offered him the position of rector in the Latin school of Leer (later renamed the Ubbo-Emmius-Gymnasium). Whilst remaining in Leer it is known that Emmius had corresponded with many other important people of the time who had fled from Groningen after the area fell into the hands of the Spanish. When Groningen surrendered to Prince Maurits in 1594 those who fled returned and offered Ubbo the position of rector in St Maarten school. When in 1614 the decision was made to form a university, under the guidance of Emmius. As a result, he was chosen as the principal and professor of history and Greek and ultimately became the first rector magnificus of the Academy in which he formed.