Admitted to the bar in 1533, Bacon was made attorney of the court of wards and liveries in 1546. Despite his Protestant sympathies, he retained his office during the reign of the Roman Catholic queen Mary I (1553–58). Upon the accession of Elizabeth, Bacon was made lord keeper of the great seal.

In this position he worked with Elizabeth's chief minister, Sir William Cecil (later Lord Burghley), to maintain the relatively moderate Protestantism of the Elizabethan church. At the same time, Bacon advocated policies designed to undermine the power of Catholics in Europe. He was temporarily dismissed from court after a misunderstanding with the queen in 1564, but he soon regained his former influence. Bacon's distrust of the Catholic Mary Stuart, who was imprisoned in England, led him in 1570 to oppose effectively a plan to reinstate her on the Scottish throne.