In March 1567 Mary, Queen of Scots granted her "well-beloved clerk and counsellor" the reward of a 19 lease or tack of her incomes from the Parsonage of Glasgow and the lands of Provand.
On 6 December 1567, he was deprived of this office, in favour of Sir James Balfour, by Regent Moray, on the pretext that the act of institution required it to be held by a person of the spiritual estate.
Balfour was in turn removed in 1568, when he was accused of participation in Darnley's murder, and Baillie, being reinstated, held the office till his death, 26 May 1593.
After the Scottish Reformation, Provan Hall near Glasgow became a residence of William Baillie.
She passed the ownership of Provan Hall to their eldest son, Francis Hamilton of Silvertonhill in 1599.