Mr. Duncan was settled minister at Crail, in the shire of Fyfe, and was afterwards summoned before the high commission court at St. Andrews, in the year 1619. on account of his faithfulness in opposing the five articles of Perth. At the first time of his compearance, he declined their authority; and at the second, he adhered to his former declinature, upon which the high commission court passed the sentence of deposition against him, and ordained him to enter himself in ward at Dundee. After the sentence was pronounced, he gave in a protestation, which was as follows, "Now, seeing I have done nothing of this business, whereof I have been accused by you, but have been serving Jesus Christ my master in rebuking vice, in simplicity and righteousness of heart. I protest (seeing ye have done me wrong) for a remedy at God's hand, the righteous Judge, and summon you before his dreadful judgment-seat, to be censured and punished for such unrighteous dealings, at such a time as his majesty shall think expedient, and, in the mean time decline this your judgment simpliciter now as before, and appeal to the ordinary assembly of the church, for reasons before produced in write. Pity yourselves for the Lord's sake; lose not your own dear souls, I beseech you for Esau's pottage: Remember Balaam, who was cast away by the deceit of the wages of unrighteousness; forget not how miserable Judas was, who lost himself for a trifle of money, that never did him good. Better be pined to death by hunger, than for a little pittance of the earth, to perish for ever, and never be recovered, so long as the days of heaven shall last, and the years of eternity shall endure. Why should ye distress your own brethren, sons and servants of the Lord Jesus; this is not the doing of the shepherds of the flock of Christ: if ye will not regard your souls nor consciences, look I beseech you, to your fame, why will ye be miserable both in this life and in the life to come."

When the bishop of St. Andrews had read some few lines of this admonition, he cast it from him, the bishop of Dumblane took it up, and reading it, said he, calls them Esau's, Balaams and Judases "Not so, said Mr. Duncan, read again, beware that ye be not like them." In the space of a month after, he was deposed for non-conformity.

In the month of July 1621, he presented a large supplication, in name of himself, and some of his faithful brethren, who had been excluded the general assembly, to Sir George Hay clerk register, on which account he was in a few days after, apprehended by the captain of the guards, and brought before the council, who accused him for breaking ward, after he was suspended and confined to Dundee, because he had preached the week before at Crail. Mr. Duncan denied that he had been put to the horn; and as for breaking ward, he said, That, for the sake of obedience, he staid at Dundee, separated from a wife and six children for a half a year, and the winter approaching forced him to go home. In the end, he requested them not to imprison him on his own charges, but the sentence had been resolved on before he compeared. He was conveyed to Dumbarton castle next day (some say to Blackness castle); here he remained until the month of October thereafter, when he was again brought before the council, and by them was confined to Kilrinnie, upon his own charges; This was a parish neighbouring to his own. Upon another occasion, of the same nature with this just now narrated, this worthy man was banished out of the kingdom, and went to settle at Berwick, but having several children, and his wife big with another, they were reduced to great hardships, being obliged to part with their servant, they had scarcely subsistence sufficient for themselves. One night in particular, the children asking for bread, and there being none to give them, they cried very sore; the mother was likewise much depressed in spirit, for Mr. Duncan had resource sometimes to prayer, and in the intervals endeavoured to cherish his wife's hope, and please the children, and at last got them to bed, but she continued to mourn heavily. He exhorted her to wait patiently upon God, who was now trying them, but would undoubtedly provide for them, and added, that if the Lord should rain down bread from heaven, they should not want. This confidence was the more remarkable, because they had neither friend nor acquaintance in that place to whom they could make their case known. And yet before morning, a man brought them a sackful of provision, and went off without telling them from whence it came, though entreated to do it. When Mr. Duncan opened the sack, he found in it a bag with twenty pounds Scots, two loaves of bread, a bag of flour, another of barley and such-like provisions; and having brought the whole to his wife, he said, "See what a good master I serve." After this she hired a servant again, but was soon reduced to a new extremity; the pains of child-bearing came upon her, before she could make any provision for her delivery, but providence interposed on their behalf at this time also: While she travailed in the night-season, and the good man knew not where to apply for a midwife, a gentlewoman came early in the morning riding to the door, and having sent her servant back with the horse, with orders when to return. She went in, and asked the maid of the house, How her mistress was, and desired access to her, which she obtained; she first ordered a good fire to be made, and ordered Mrs. Duncan to rise, and without any other assistance than the house afforded, she delivered her, and afterwards accommodated Mrs. Duncan and the child with abundance of very fine linen, which she had brought along with her. She gave her likewise a box, containing some necessary cordials and five pieces of gold, bidding them both be of good comfort, for they should not want. After which, she went away on the horse, which was by this time returned for her, but would not tell her name, nor from whence she came.

Thus did God take his own servant under his immediate care and providence, when men had wrongfully excluded him from enjoying his worldly comforts. He continued zealous and stedfast in the such, and, to the end of his life, his conduct was uniform with the circumstances of this narrative.