Elizabeth de St Michel was born at Bideford, Devon, on 23 October 1640. She was the daughter of Alexandre le Marchant de St Michel and Dorothea Fleetwood. The family lived in Devon, where Dorothea had inherited land. They later lost this property and subsequently travelled between Germany, Flanders, and Ireland. Dorothea, along with Elizabeth and her brother Balthasar, fled to Paris after their fortunes had been undermined by Alexandre's increasingly determined religious views. Her mother intended that Elizabeth should become a nun, and she was briefly placed in the city's Ursuline convent before she and Balty were removed to London by their father.
It was in London that Elizabeth met Samuel Pepys, then in the employ of Edward Mountagu, later first earl of Sandwich. Details of the circumstances of their meeting remain unknown, though it is evident, given that neither party stood to gain financially from the union, that theirs was a love match. The couple were married at a civil service at St Margaret's, Westminster, on 1 December 1655, when Elizabeth, described as being of St Martin-in-the-Fields, was aged fifteen and Samuel twenty-two. By the time of this service the couple had apparently already 'married' in an unrecorded religious ceremony which took place on 10 October, the date Pepys identified as their anniversary during his years of diary keeping.
The early months of their marriage were characterised by antagonism and argument. The cramped conditions of his attic apartment at Whitehall Palace exacerbated both Elizabeth's irritation at the prosaic nature of married life and Samuel's jealousy and sexual frustration which derived, in part, from his own and his wife's recurrent ill health. Within a year of their marriage Elizabeth left her husband to stay with her family at Charing Cross returning to Whitehall in December 1657. In August of the following year the couple left for a house in Axe Yard, Westminster, where they stayed until July 1660 before moving to the Navy Office at Seething Lane.
By this date Pepys had begun a diary, which he maintained daily until six months before his wife's death. Pepys never named her in his journal but referred to 'his wife'.
Elizabeth gained additional leisure time as her husband's career, and salary, improved over the decade. She also enjoyed more freedom than many women of her status on account of the marriage remaining childless.
In June 1669 Elizabeth accompanied her husband and brother on a tour of northern France and the Netherlands. Here she contracted the fever, probably typhoid, which developed during their return journey and from which, aged twenty-nine, she died at Seething Lane on 10 November.