In this search, Sir Robert was very successful, recovering many important papers used by the archbishop, and discovering at Rome the Black Book of Paisley, a manuscript of great value.
After spending nine years abroad, Spottiswood returned home, and was received with favour by James VI, who appointed him privy councillor on 25 June 1622.
His speech on that occasion, in which he described the relations then existing between the bench and the bar, is printed in the memoir by his grandson, John Spottiswood (1666–1728), in his edition of Sir Robert's 'Practicks,' and in the first volume of the 'Spottiswoode Miscellany.'
Sir Robert was one of the crown assessors for the trial of John Elphinstone, Lord Balmerino in 1634 and it was afterwards alleged – without much foundation – that he gave a partial and unfair aspect to the case.
His attitude was so distinctly against the Covenanters that, in 1638, when the Scottish Episcopal Church was abolished by the general assembly, he was forced to flee to England, where he remained until Charles I made his second visit to Scotland.
Sir Robert set out from Oxford with this warrant, travelled through Wales to the Isle of Man, shipped thence to Lochaber, and, meeting Montrose in Athol, where he gave him the Royal commission.
In his own defense, Sir Robert pleaded that he had taken the office of secretary at the King's command, temporarily and by necessity, and he urged that, though he had been with Montrose, he had not borne arms, and also that he had received promise of quarter before he surrendered.
While Wishart describes him as an Episcopalian martyr whose chief crime was being the son of Archbishop Spottiswoode, Baillie denounces him as a partial and corrupt judge, and seems to regard his violent end as a meet punishment for his alleged unfairness to Lord Balmerino.