He was educated in Scotland and in Collegium Romanum in Rome, where on 19 August 1563 he became a jesuit. From 1564 he lived in Braniewo (Royal Prussia), where he was professor of grammar in the biggest Polish jesuit collegium and a novice master. In 1565 he was ordained a priest. In Braniewo he was in constant contact with Cardinal Stanislaus Hosius. He was considered a good priest, but learning Polish was difficult to him, and he had some problems with the finances of the school. Due to these problems he was permitted to leave Poland in 1580, when he met the Scottish king for the first time. In September 1580 he went back to Poland - from 1580 to 1587 he performed similar tasks in Kraków, Poznań and Wilno. In 1587 he left Poland and went back to Scotland. During the journey to Scotland in 1580 and during his second stay there he was organizing transports of Scottish youths to be trained in Polish schools.
Abercromby was brought into prominence chiefly by the fact that he is said to have converted the Queen of James I of England, when that monarch was as yet James IV of Scotland. The Queen was Anne of Denmark, and her father, an ardent Lutheran, had stipulated that she should have the right to practice her own religion in Scotland, and for that purpose sent with her a chaplain named John Lering who, however, shortly after his arrival, became a Calvinist. The Queen, who abhorred Calvinism, asked some of the Catholic nobles for advice, and it was suggested to call Father Abercromby, who, with some other Jesuits, was secretly working among the Scottish Catholics and winning many illustrious converts to the Church. Though brought up a Lutheran, Queen Anne had in her youth lived with a niece of the Emperor Charles V, and not only knew something of the faith, but had frequently been present at mass with her former friend. Abercromby was introduced into the palace, instructed the Queen in the Catholic religion, and received her into the Church. This was about the year 1600. As to the date there is some controversy. Andrew Lang, who merely quotes MacQuhirrie as to the fact of the conversion, without mentioning Abercromby, puts it as occurring in 1598. Intelligence of it at last came to the ears of the King, who, instead of being angry, warned her to keep it secret, as her conversion might imperil his crown. The king first supported Abercromby and arranged for him to stay near Anne. James even went as far as to appoint Abercromby Superintendent of the Royal Falconry, in order that he might remain near the Queen. Up to the time that James succeeded to the crown of England, Father Abercromby remained at the Scottish court, celebrating Mass in secret, and giving Holy Communion nine or ten times to his neophyte. Anne herself gave proof of her devotion, during their crowning. When the King and Queen were crowned sovereigns of Great Britain, Anne gave proof of her sincerity by absolutely refusing to receive the Protestant sacrament, declaring that she preferred to forfeit her crown rather than take part in what she considered a sacrilegious profanation. Of this, Lang, in his History of Scotland, says nothing. She made several ineffectual attempts to convert the King.
Abercromby remained in Scotland for some time, but as a price of 10,000 crowns was put upon his head he came to England, only to find that the King's kindly dispositions toward him had undergone a change. The alleged discovery of a Gunpowder Plot in 1605, and the attempts made to implicate the Jesuits in the conspiracy had excited in the mind of the King feelings of bitter hostility to the Society of Jesus. He ordered a strict search to be made for Abercromby, who consequently fled England and went back to Braniewo, where he died in 1613.