However, on the accession of her younger sister Elizabeth in 1558, he was appointed Lord Keeper of the Great Seal, largely owing to the influence of his brother-in-law William Cecil.

Bacon helped secure the position of Archbishop of Canterbury for his friend Matthew Parker, and in his official capacity presided over the House of Lords when Elizabeth opened her first parliament.

Bacon's innocence having been admitted, he was restored to favour, and replied to a writing[clarification needed] by Sir Anthony Browne, who had again asserted the rights of the House of Suffolk, to which Lady Katherine belonged.

He thoroughly distrusted Mary, Queen of Scots; objected to the proposal to marry her to Thomas Howard, 4th Duke of Norfolk; and warned Elizabeth that serious consequences for England would follow her restoration.

He seems to have disliked the proposed marriage between the English queen and François, Duke of Anjou, and his distrust of the Roman Catholics and the French was increased by the St Bartholomew's Day massacre.