In Scotland
In 1577 he was appointed ambassador in Scotland, where he had difficult tasks to perform: to counteract the influence of France, retain a hold on James VI, keep together a party that was favourable to England, and promote disunion among the Scottish nobles. In 1578 he managed by his tact to compose a quarrel between James Douglas, 4th Earl of Morton and the privy council which threatened to plunge Scotland into civil war. In 1581 he was busily employed in endeavouring to counteract the growing influence of Esme Stewart, lord of Aubigné, over James VI. He witnessed the events which led to the raid of Ruthven and D'Aubigné's fall. He tried hard to gain possession of the casket letters, which after Morton's death were said to have come into the hands of John Ruthven, 3rd Earl of Gowrie, but his attempts failed.
In April 1583 he gave gold chains as gifts to two secret Scottish contacts of Francis Walsingham. He thought that James VI was trying to get rid of him by employing Lord Doune. He managed to procure his recall from in 1583, but he still held the post of treasurer of Berwick, and was often employed on diplomatic missions in Scotland.
Bowes took delivery of £3000 subsidy money that Elizabeth I paid to James VI in 1588 and gave it to John Carmichael at Cawmills (now Edrington). In 1588 or 1589 a Scottish diplomat in London, Samuel Cockburn of Templehall, husband of the poet Elizabeth Douglas, sent him household goods and clothing by sea but the ship was taken by pirates.
Bowes met the bride of James VI, Anne of Denmark on 3 May 1590 at her lodging in the King's Wark at Leith. He told her Queen Elizabeth was pleased with her letters, and she said she was thankful for the favour and goodwill she found in Elizabeth's letter to her.
Bowes attended St Giles Kirk and the town council provided velvet cushions for his and his wife Eleanor Bowes' seats in the loft or gallery. He had a chest in his Edinburgh lodging which contained copies of the family trees of the Scottish nobility. His servant George Nicholson made copies of these for Burghley. Eleanor Bowes had the key of the chest.
Bowes lodged in the house of the Fowler family, which belonged to the widow Janet Fockart. In the early 1590s Giacomo Castelvetro, an Italian writer who served James VI as a language tutor and secretary, lodged with them and Eleanor Bowes made friends with his wife, Isotta de Canonici, the widow of Thomas Erastus.
Some of the information he sent to England came from Scottish informers who he called "talesmen".
