John Stewart, 3rd Earl of Buchan, son and heir of Alexander, succeeded to the Earldom in 1505. He was retoured heir to his father in the Earldom and Earlshill in 1519; until then he retained the style of Master of Buchan which he had held in his father's lifetime. On his own resignation, a charter of all his lands, baronies, lordships, and heritable offices, and of the Earlshill, was granted 4 August 1547 to his son John Stewart and his heirs, reserving the Earl's liferent.

He married Margaret, daughter of James Scrymgeour of Dudhope, Constable of Dundee, by whom he had:

• John Stewart, Master of Buchan, who married, first, Mary, only child of James Stewart, 1st Earl of Moray
  James Stewart, 1st Earl of Moray (1501 creation)
  James Stewart, Earl of Moray was the illegitimate son of James IV of Scotland and his mistress Janet Kennedy. He was created Earl of Moray in 1501, and was young enough to avoid fighting at the disastrous Battle of Flodden Field in 1513. He went on to have a varied relationship with his...
  
  , an illegitimate son of King James IV
  James IV of Scotland
  James IV was King of Scots from 11 June 1488 to his death. He is generally regarded as the most successful of the Stewart monarchs of Scotland, but his reign ended with the disastrous defeat at the Battle of Flodden Field, where he became the last monarch from not only Scotland, but also from all...
  
   and Janet Kennedy
  Janet Kennedy
  Janet Kennedy , the first daughter of John Kennedy, 2nd Lord Kennedy, became a mistress of King James IV of Scotland.Through her father, she was a great-great-granddaughter of King Robert III...
  
  ; secondly, Margaret, daughter of Walter Ogilvy of the Boyne, who survived her husband by two years at least. He was killed in the Battle of Pinkie Cleugh
  Battle of Pinkie Cleugh
  The Battle of Pinkie Cleugh, on the banks of the River Esk near Musselburgh, Scotland on 10 September 1547, was part of the War of the Rough Wooing. It was the last pitched battle between Scottish and English armies, and is seen as the first modern battle in the British Isles...
  
  , 10 September 1547, leaving an only child by Margaret Ogilvy,
  • Christina Stewart
    Christina Stewart, 4th Countess of Buchan
    Christina Stewart, Countess of Buchan in her own right, succeeded her grandfather, John Stewart, 3rd Earl of Buchan, in 1551. In that year she was, as heir to her father, enfeoffed in the lands, jurisdictions, and offices enumerated in her grandfather's charter of 1547...
    
    , later to become Countess of Buchan.

• James Stewart, Master of Buchan in 1547, after his brother's death. He married Christian, daughter of John Strang of Balcaskie, by whom he had:
  • James Stewart, served as heir to his father, 13 October 1604, and to his grandfather, great-grandfather, and great-great-grandfather 26 March 1618.
  • Alexander Stewart.
  • Margaret Stewart, married to Sir Hadrian Damon of Birtewelte in Denmark.
  • Isobel Stewart.

John Stewart is spoken of as recently dead in 1551. However his first son and heir had predeceased him, so title of the Earldom devolved to his granddaughter Christina.