Before 10 December 1558 Montagu married Magdalen Dacre, by whom he had three sons, Sir George, Thomas and Henry, and three daughters, Elizabeth, Mabel and Jane.

[9] Mary and Southampton continued on affectionate terms until about 1577, but by then he had forbidden her to see a man named Donsame, described as "a common person", and after that development the couple's relationship worsened.

There then arose a dispute between Southampton and his father-in-law over his treatment of his wife, which years later Robert Persons blamed on the Roman Catholic conspirator Charles Paget.

Yett will I do my parte so longe as I am with him, but good my Lorde, procure so soone as conveniently yowe may, some end to my miserie for I am tyred with this life.

In his Will, Southampton named Thomas Dymock and Charles Paget as executors, and Mary contested this with some success, supported by the Earl of Leicester.

Howard then transferred the custody to Lord Burghley, but kept control of the young peer's estates, and as a result late in 1581 or early in 1582 the new Earl of Southampton, then aged eight, came to live at Cecil House in the Strand.

She left a will proved on 14 November in which she gave instructions for her burial at Titchfield "as near as may be unto the body of my honorable and dearlie beloved Lord and husband Henrie late Earle of Southampton".