In 1534, Mary secretly married a commoner and the second son of an Essex landowner, William Stafford. Since Stafford was a soldier, his status was so much beneath hers, his prospects as a second son were so slight, and he was possessed such a small income, many believe the union was a love match. When Mary became pregnant, the marriage was discovered. Queen Anne was furious, and the ambitious Boleyn family disowned Mary. The couple were banished from court.
Mary's financial circumstances became so desperate that she was reduced to begging the King’s adviser Thomas Cromwell to speak to Henry and Anne on her behalf. She admitted that she might have chosen 'a greater man of birth and a higher', but never one that should have loved her so well, nor a more honest man. And she went on, 'I had rather beg my bread with him than to be the greatest queen in Christendom. And I believe verily ... he would not forsake me to be a king.' Henry, however, seems to have been indifferent to her plight. Mary asked Cromwell to speak to her father, her uncle, and her brother, but to no avail. It was Anne who relented, sending Mary a magnificent golden cup and some money, but still refusing to receive her at court. This partial reconciliation was the closest the two sisters attained; it is not thought that they met after Mary's court exile.
Mary's life between 1534 and her sister's execution on 19 May 1536 is difficult to trace. There is no record of her visiting her parents, nor did she visit her sister Anne or her brother George when they were imprisoned in the Tower of London, nor is there evidence of any correspondence. Like their uncle, Thomas Howard, 3rd Duke of Norfolk, she may have thought it wise to avoid association with her now-disgraced relatives.
Mary and her husband remained social outcasts, living in retirement at Rochford Hall in Essex, which was owned by the Boleyns. After Anne’s execution, their mother retired from the royal court, dying in seclusion just two years later. Her father, Thomas, died the following year. Following the deaths of her parents, Mary inherited some property in Essex. She seems to have lived out the rest of her days in obscurity and relative comfort with her second husband. She died in her early forties, on 19 July 1543.