He found a home in the Low Countries, where he wrote his great work, the Altare Damascenum which was an attack on Anglican episcopacy.

It was the time when King James was attempting to introduce prelacy into the Church of Scotland, and Calderwood was one of the sturdiest opponents of the royal scheme.

Calderwood openly protested against the jurisdiction of the bishop, for which offence he was deprived of his right to attend church courts, and required to confine himself to the limits of his parish, Silenced in this way and prevented from taking any part in public proceedings, he applied himself the more earnestly to the authority.

The matter ended in Calderwood being deprived of his charge, confined first in the prison of St Andrews and then of Edinburgh, and finally ordered to leave the country.

Here he had a severe attack of illness, and a rumour of his death was published along with a pretended recantation of his views, and an invitation to all to accept the "uniformity of the kirk".

‘It was,’ says Thomson, in his life of Calderwood, prefixed to the Wodrow Society's edition of his history, ‘the great storehouse from which the prelatic arguments were subverted, and conversions to presbyterianism effected during the period of the second Scottish reformation.

… It will only be from a correct translation of the "Altare Damascenum" that the public can derive a full idea of the eloquence, learning, and acute dialectic power of its author.’[5] After Calderwood's return in 1625 to Scotland from Holland, he remained for some time without a charge.

He was employed, along with David Dickson and Alexander Henderson, in the drawing up of the Directory for Public Worship, which continued to be the recognised document for regulating the service in the Church of Scotland.

When he had reached his seventy-third year, the general assembly, for the purpose of enabling him to perfect his work, granted him an annual pension of eight hundred pounds Scots.

His papers were bequeathed to a brother's family, a member of which, William Calderwood, Lord Polton, presented the manuscripts of his history to the British Museum on 29 January 1765.

[7] He continued to take an active part in the affairs of the church, and introduced in 1649 the practice, now confirmed by long usage, of dissenting from the decision of the General Assembly, and requiring the protest to be entered in the record.