She had separate 10-minute audiences at Hillsborough Castle with Stormont First Minister Peter Robinson and Deputy First Minister Mr McGuinness.
It was the Queen's third encounter with the Sinn Fein veteran and former IRA commander but their first one-to-one meeting.
It provided more evidence of efforts to normalise relations between Irish republicans and the British establishment in the post conflict era.
Further proof will be exhibited when Mr McGuinness accompanies the Royal couple on a tour of the old Crumlin Road Gaol in Belfast - a prison the politician was detained in himself during the Troubles.
While relations between Sinn Fein and the Royal family are seemingly thawing, a deep freeze has set in at the heart of the power-sharing institutions at Stormont.
Political progress on big ticket issues has stalled, with Mr McGuinness and Democratic Unionist leader Mr Robinson unable to find consensus on how to deal with the long-standing disputes - such as those on parades and flags - that continue to block the road to a fully shared society.
As with a range of recent royal engagements involving Ireland, both north and south, the themes of reconciliation, regeneration and focusing on the future will be emphasised during what is the Queen and Duke's 21st visit to Northern Ireland.
They landed earlier yesterday at George Best Belfast City Airport to be met by Northern Ireland Secretary Theresa Villiers and former Olympic champion and now Lord Lieutenant of Belfast Dame Mary Peters.
The couple then went to Hillsborough Castle, their official residence. Crowds in the Co Down town cheered and waved flags.
Itineraries for previous Royal visits have been kept secret due to security fears, but this week's engagements have been publicised.