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. Though an implacable enemy of Mary Queen of Scots, he opposed Cecil's policy of war against France, on financial grounds; but he favoured closer links with foreign Protestants, and was aware of the threat to England from the alliance between France and Scotland. In 1559 he was authorized to exercise the full jurisdiction of lord chancellor. In 1564 he fell temporarily into the royal disfavour and was dismissed from court, because Elizabeth suspected he was concerned in the publication of a pamphlet, " A Declaration of the Succession of the Crowne Imperial of Ingland," by John Hales, which favoured the claim of Lady Catherine Grey (sister of Lady Jane Grey) to the English throne. Bacon's innocence having been admitted, he was restored to favour, and replied to a writing by Sir Anthony Browne, who had again asserted. He objected to the proposal to marry Mary, Queen of Scots to the duke of Norfolk; and warned Elizabeth that serious consequences for England would follow her restoration. He also disapproved of the proposed marriage between the English queen and Francis, duke of Anjou, and his distrust of the Roman Catholics and the French was increased by the St Bartholomew's Day massacre. As a loyal English churchman he was ceaselessly interested in ecclesiastical matters, and made suggestions for the better observation of doctrine and discipline in the church.
He died in London and was buried in St Paul's Cathedral, his death calling forth many tributes to his memory. He had been an eloquent speaker, a learned lawyer, a generous friend; and his interest in education led him to make several gifts and bequests for educational purposes, including the foundation of a free grammar school at Redgrave. He was twice married and by his first wife, Jane, had three sons and three daughters. His second wife was Anne (d. 1610), daughter of Sir Anthony Cooke, by whom he had two sons. Bacon's eldest son, Nicholas (c. 1540-1624), was member of parliament for the county of Suffolk and in 1611 was created premier baronet of England. This baronetcy is still held by his descendants. His second and third sons, Nathaniel (c. 1550-1622 and Edward (c. 1550-1618), also took some part in public life, and through his daughter, Anne, Nathaniel was an ancestor of the marquesses Townshend. His sons by his second wife were Anthony Bacon and Francis Bacon.\n