Margaret of Anjou at Lichfield ordered Stanley to raise forces to intercept him. However, when the two armies met at the Battle of Blore Heath in 1459, though only a few miles away, Stanley kept his 2,000 men out of the fight. His brother, Sir William Stanley, who was certainly in the Yorkist army was subsequently attainted.
Yet by 1460 Lord Stanley had begun to co-operate with the Yorkist lords who by this time had possession of the King and ruled in his name, and he rapidly consolidated his association with the new regime. In the early 1460s he joined his brother-in-law, Warwick, in the campaigns against the Lancastrian forces and Stanley was confirmed in his fees and offices as the new King, Edward IV, needed him to secure the north-west. In the late 1460s, however, the coalition that had brought the Yorkist Edward to the throne was fracturing and Stanley found his loyalties divided once again. “The dramatic shifts in political fortune between 1469 and 1471, and their impact on the tangled networks of affinity and allegiance, are hard to unravel.” When Warwick, fleeing before Edward in 1470, made his way to Manchester in the hope of support, Stanley was not forthcoming, but on Warwick's return he lent him armed support in the restoration of the House of Lancaster and of Henry VI. Lord Stanley was soon forgiven for his disloyalty. After the restoration of Edward IV in 1471, he was appointed steward of the king's household and thereafter became a regular member of the royal council. Yet, the death of his first wife, Eleanor Neville at this period severed his connection with Warwick and the Nevilles and allowed in 1472 a marriage of still greater political significance. His new wife, Lady Margaret Beaufort, dowager Countess of Richmond, was the mother of Henry Tudor – potential heir of the House of Lancaster. Militarily during this period, and now a stalwart of the Yorkist regime, Stanley led several hundred men in the expedition to France in 1475 and in 1482 served with a large company in the campaign of the Duke of Gloucester (later Richard III) in Scotland, playing a key role in the capture of Berwick upon Tweed.
After the unexpected death of Edward IV in 1483 and the accession of his twelve-year-old son Edward V, Stanley was among those who sought to maintain a balance of power between the young king's uncle, Richard, Duke of Gloucester, who was now Lord Protector, and his maternal family, the Woodvilles. (Stanley’s own son and heir, George Stanley, Lord Strange was married to Joan Le Strange whose mother was Jacquetta Woodville, the Queen’s mother). When Gloucester attacked this group at a council meeting in June 1483, Stanley was wounded and imprisoned but at least spared the fate of Lord Hastings – that of summary execution. That month, Parliament declared Edward V and his younger brother Richard, Duke of York (the Princes in the Tower) illegitimate on the grounds that their father Edward IV's marriage to Elizabeth Woodville was bigamous, by way of a prior pre-contract of marriage with Eleanor Butler. The Duke of Gloucester was therefore declared king Richard III by public acclamation, later confirmed by Parliament under the Act Titulus Regius.
Apparently “in preparing the ground for the usurpation and in consolidating his position, Richard found it more expedient to appease than to alienate the house of Stanley.” Thus, Lord Stanley was soon at liberty and continued as steward of the royal household, apparently flourishing at the heart of the new regime. He bore the great mace at Richard's coronation, while his wife carried the new queen’s train. Richard stripped Stanley's wife Margaret Beaufort of all her titles and possession for her part "in compassyng and doyng Treason", but transferred all her properties to Stanley, effectively negating much of the punishment.
