During the crisis of the Scottish Reformation in 1559, Robert Logan Senior took his Leith followers to face the French troops of Henri Cleutin at Cupar Muir.
[3] Robert's first wife, Elizabeth Makgill, after their divorce married Sir Thomas Kennedy of Culzean, Tutor of Cassilis.
In 1430, an ancestor, also called Sir Robert Logan (d. 1439), and his wife Dame Katherine founded the monastery of St Anthony which was near South Leith Parish Church with an outlying chapel at Arthur's Seat in Holyrood Park, which survives as a ruin.
[5] Robert inherited Fast Castle and other lands near the border with England, as "nephew" and heir of Elizabeth Martene, Lady Fastcastle, widow of Cuthbert Home who had fallen at Flodden Field.
On 5 April 1603, James VI of Scotland raised the status of the Restalrig estate into a free barony, which gave Robert extra jurisdictions over his tenants.
James VI had hoped that Archibald Douglas, a Scotsman resident in London but not an accredited ambassador, might be able to intervene to save his mother from execution after the revelation of the Babington plot in 1586.
It is indeid of treuthe that the Kinge is in greit anger at you and altogither be Williame Keithe and James Hetson's informatioune, and thinks ye have done hem wronge... His Majesty taks the daithe of his mother very hevely, and hes, for that cause, retirit hemself to Dalkethe for the space of 10 days in quyet".Modernised: "he wrote to me, desiring me to write to your lordship that you should write no more to him, for your letters do him very much harm, and he was nothing the wiser from your intelligence.
It is indeed of truth that the King is in great anger at you, and altogether by William Keith and James Hudson's information, and thinks you have done him wrong.... His Majesty takes the death of his mother very heavily, and has for that cause, retired himself to Dalkeith Palace for the space of 10 days in quiet".
[12] Logan was implicated in an alleged attempt to abduct James VI of Scotland by John Ruthven, 3rd Earl of Gowrie in Perth on 4 August 1600 by the confession of George Sprot of Eyemouth.
In 1609 the King's advocate Thomas Hamilton wrote that credible witnesses including kirk ministers and others recognised Logan's handwriting in the "treasonable missives".