In 1577 Francken left his position as professor of the Jesuit college in Vienna and commenced the publication from Basel and La Rochelle of many tracts against the order.
[1] François Du Jon in 1584 wrote his Defensio catholicae doctrinae de s. trinitate personarum in unitate essentiae Dei, adversus Samosatenicos errores against Francken.
Later, on October 13, 1592, Dee would show Franken's book of "blasphemie" (Poland 1585) to John Whitgift, the Archbishop of Canterbury, desiring it be confuted.
[4] Francken worked alongside Francis David, Johannes Sommer, Jacob Palaeologus as lector at the Unitarian Gymnasium in Cluj (German: Klausenburg, Hungarian: Kolozsvár, Latin: Claudiopolis) in 1585 and between 1589 and 1591.
In 1598 Francken travels to Italy in the company of papal delegate Cesare Speciano, where he was arrested and imprisoned by the Inquisition.