After schooling in Pforzheim, where he established a friendship with Philipp Melanchthon, he studied theology in Cologne. He was a teacher in Rottweil in 1510 and in Bern in 1513. In 1520 he became a canon and the people’s priest.
In 1526, he participated in the disputation of Baden. In 1528 the Bern disputation took place, the result of which the Bernese Reformation edict was issued on 7 February 1528 where Bern officially decided for the Reformation.
Zwingli's 1531 death brought the Reformation in Bern to a crisis, to which the city council called for the first Bernese synod with 200 participants gathering. Haller was especially concerned as Zwingli's successor Heinrich Bullinger was unable to attend the synod. However, he received strong support from Wolfgang Capito who arrived in Bern shortly before the opening of the Synod.
In 1532 Haller became of the leader of the Reformed Church of Bern. He was in contact with Guillaume Farel in the western part of Switzerland and Heinrich Bullinger in Zurich and acted as a mediator between the Calvinist Reformation and Zurich.