He was settled minister at Kinghorn, in the shire of Fyfe, and went as chaplain with King James in the year 1590, to Denmark, when he brought home his queen. He was afterwards concerned in several important affairs of the church, until that fatal year 1618, when the five articles of Perth were agreed on in an assembly held at that place. He attended at this assembly, and gave in some proposals[48], upon being (along with others of his faithful brethren) excluded from having a vote by the prevailing party of that assembly.

In 1620, he was with some others, summoned before the high commission-court, for not preaching upon holy days, and not administring the communion conform to the agreement at Perth, with certification if this was proven, that he should be deprived of exercising the functions of a minister in all time coming. But there being none present on the day appointed, except the bishops of St. Andrews, Glasgow and the isles, and Mr. Walter Whiteford, they were dismissed at that time; but were warned to compear again on the first of March. The bishops caused the clerk to exact their consent to deprivation, in case they did not compear against that day. Nevertheless, they all protested with one voice, That they would never willingly renounce their ministry, and such was the resolution and courage of Mr. Scrimzeor, that notwithstanding all the threatening of the bishops, he celebrated the communion conform to the antient practice of the church, a few days thereafter.

On the day appointed for their next compearance, the bishops of St. Andrews, Dunkeld, Galloway, the isles, Dumblain, Mr. Hewison commissary of Edinburgh, and Dr. Blair, being assembled in the bishop of St. Andrews lodging in Edinburgh, Mr. John Scrimzeor was again called upon to answer, and the bishop of St. Andrews alleged against him, that he had promised either to conform or quit his ministry, as the act at his last compearance on January 26th reported; he replied, "I am fore straitned, I never saw reason to conform; and as for my ministry, it was not mine and so I could not quit it." After long reasoning betwixt him and the bishops, concerning church policy and the keeping of holy days, he was removed for a little. Being called in again, the bishop of St. Andrews told him, "You are deprived of all function within the kirk, and ordained within six days to enter in ward at Dundee." "It is a very summary and peremptory sentence," said Mr. Scrimzeor, "ye might have been advised better, and first have heard what I would have said." "You shall be heard," said the bishop. This brought on some further reasoning, in the course of which Mr. Scrimzeor gave a faithful testimony against the king's supremacy over the church, and among other things said, "I have had opportunity to reason with the king himself on this subject, and have told him that Christ was the sovereign, and only director of his house; and that his majesty was subject to him. I have had occasion to tell other mens matters to the king, and could have truly claimed this great preferment." "I tell you Mr. John," said the bishop of St. Andrews, "that the king is pope, and shall be so now;" He replied, "That is an evil style you give him:" And then gave in his reasons in write, which they read at leisure. Afterwards the bishop of St. Andrews said to him, "Take up your reasons again, if you will not conform, I cannot help it; the king must be obeyed, the lords have given sentence and will stand to it." "Ye cannot deprive me of my ministry," said Mr. Scrimzeor, "I received it not from you; I received it from the whole synod of Fyfe, and, for any thing ye do, I will never think myself deposed." The bishop of St. Andrews replied, "You are deprived only of the present exercise of it." -- Then he presented the following protestation, "I protest before the Lord Jesus, that I get manifest wrong; my reasons and allegations are not considered and answered. I attest you to answer at his glorious appearance, for this and such dealings, and protest that my cause should have been heard as I pled, and still plead and challenge. I likewise appeal to the Lord Jesus, his eternal word, to the king my dread sovereign, his law, to the constitution of this kirk and kingdom, to the councils and assemblies of both, and protest that I stand minister of the evangel, and only by violence I am thrust from the same." "You must obey the sentence," said the bishop of St. Andrews; he answered, "That Dundee was far off, and he was not able for far journeys, as physicians can witness." And he added, "Little know ye what is in my purse." "Then where will you choose the place of your confinement," said the bishop: He answered, "At a little room of my own called Bowhill, in the parish of Auchterderran." Then said the bishop, "Write, At Bowhill, during the king's pleasure." Thus this worthy servant of Christ lived the rest of his days in Auchterderran. In his old age he was grievously afflicted with the stone. He said to a godly minister, who went to see him a little before his death, "I have been a rude stunkard all my life, and now by this pain the Lord is humbling me to make me as a lamb, before he take me to himself."

He was a man somewhat rude-like in his clothing, and in some of his expressions and behaviour; and yet was a very loving tender hearted man; of a deep natural judgment; and very learned, especially in Hebrew. He often wished that most part of books were burnt, except the bible, and some short notes thereon. He had a peculiar talent for comforting the dejected. He used a very familiar but pressing manner of preaching. He was also an eminent wrestler with God, and had more than ordinary power and familiarity with him, as appears from the following instances.

When he was minister at Kinghorn, there was a certain godly woman under his charge, who fell sick of a very lingering disease, and was all the while assaulted with strong temptations, leading her to think that she was a cast-away, notwithstanding that her whole conversation had put the reality of grace in her beyond a doubt. He often visited her while in this deep exercise, but her trouble and terrors still remained; as her dissolution drew on, her spiritual trouble increased. He went with two of his elders to her, and began first, in their presence, to comfort her and pray with her, but she still grew worse: He ordered his elders to pray, and afterwards prayed himself, but no relief came. Then sitting pensive for a little space, he thus broke silence, "What is this! Our laying grounds of comfort before her will not do; prayer will not do: We must try another remedy. Sure I am, this is a daughter of Abraham; sure I am, she hath sent for me, and therefore, in the name of God, the Father of our Lord Jesus, who sent him to redeem sinners; in the name of Jesus Christ, who obeyed the Father, and came to save us; and in the name of the Holy and blessed Spirit, our Quickner and Sanctifier -- I, the elder, command thee, a daughter of Abraham, to be loosed from these bonds." And immediately peace and joy ensued.

Mr. Scrimzeor had several friends and children taken away by death, and his only daughter who, at that time survived (and whom he dearly loved), being seized with the king's evil, by which she was reduced to the very point of death, so that he was called up to see her die; and finding her in this condition, he went out to the fields (as he himself told) in the night-time, in great grief and anxiety, and began to expostulate with the Lord, with such expressions as, for all the world, he durst not again utter. In a fit of displeasure he said, "Thou, O Lord, knowest that I have been serving thee in the uprightness of my heart, according to my power and measure, nor have I stood in awe to declare thy mind even unto the greatest in the time, and thou seest that I take pleasure in this child. O that I could obtain such a thing at thy hand, as to spare her." And being in great agony of spirit, at last it was said to him from the Lord, "I have heard thee at this time, but use not the like boldness in time coming, for such particulars." When he came home the child was recovered, and, sitting up in the bed, took some meat, and when he looked at her arm it was perfectly whole.