He intended a legal career, but gave it up from 1578 with Catholicism when required to cease hearing the sermons of the evangelical Huibert Duifhuis (1531–1581).
In 1580 Wtenbogaert was sent at the city's expense to study theology in Geneva and came into contact with Theodore Beza; but his sympathies were with Jacobus Arminius.
At the same time Wtenbogaert published his Tractaet, causing a controversy and, despite the conferences of 1611 and 1613, an effective schism with the Calvinist or Gomarist Counter-Remonstrant party.
Prince Maurice removed support from Wtenbogaert, and in 1617 the States decided for a synod, against the wish of the Remonstrants.
On 24 May 1619 he was banned from the Dutch Republic and his goods confiscated, the reason given being that he had introduced new views, contrary to the accepted Reformed theology.