In 1562, the Habsburg king Philip II of Spain designated Lindanus for the newly erected See of Roermond, and the following year, on 4 April, he was consecrated in Brussels by Cardinal Granvelle.
The new bishop began at once to reform his diocese, assisted in person at the Provincial Synods of Mechlin (1570) and of Leuven (1573) and carried out the Counter-Reformation laws and regulations of the Council of Trent.
In 1578, he travelled to Rome and Madrid in order to obtain justice against the chapter of Maastricht, which had refused to execute the regulations concerning the episcopal endowment, and to confer with the Pope and the king upon the measures necessary for the safeguarding of the Faith in the Low Countries.
Lindanus went to Rome again in 1584 to treat of the interests of his diocese and of the state of the Church in the Low Countries and in Germany; he insisted particularly upon the urgent necessity of replying in a scientific way to the Centuriators of Magdeburg.
He edited the academic discourses of Ruard Tapperus (1577–78), and wrote many works in Dutch for the instruction of his flock, in order to keep them from Protestantism and to refute the Confession of Antwerp of 1566.