On returning, he made a reputation for himself when he criticized the liturgy of Swedish King John III, who held somewhat Catholic beliefs despite Sweden having been Lutheran since 1531.
The king's brother Duke Charles, who later became King Charles IX, promoted Olaus to Archbishop of Uppsala in 1601. Despite his support, Martini was fundamentally in opposition to the beliefs of duke Charles, a conflict which eventually led to disputes between the two. Martini was an orthodox Lutheran, while Duke Charles is believed to have been inclined towards Calvinistic tenets—which he himself denied (see: crypto-Calvinism).
In 1606 Martini had a text published which was sharply polemising against Catholic and Calvinistic tenets.
Although he was in opposition to the king and the duke, he was considered a hard-working and trustworthy man by the University of Uppsala and by his communion.