On 5 September 2004, at a time of Maltese nationalist celebrations marking 40 years of Maltese independence, and 25 years since the closure of the British naval base, and in anticipation of the admission of Malta into the European Union, three of the four Irish Constitution lodges met together and resolved to form themselves into the Sovereign Grand Lodge of Malta.

This historic move was supported by one of the English (UGLE) lodges on the island, Count Roger of Normandy Lodge No 9285, and at a special meeting held on 30 June 2004 the lodge resolved to unite with the Irish lodges in the formation of the new Grand Lodge. The fourth Irish Constitution lodge also decided to participate.

Following these events, the Grand Lodge of Ireland, in consultation with the United Grand Lodge of England and the Grand Lodge of Scotland, acceded to the petition of the five lodges. On 18 November 2004, with the Grand Master of Ireland presiding, these 5 lodges were instituted and consecrated by the Grand Lodge of Ireland into The Sovereign Grand Lodge of Ancient Free and Accepted Masons of Malta (SGLoM).

The effect of having a Grand Lodge is that SGLoM has become the sovereign Masonic body for the Maltese islands, having inherent power and authority to form a Constitution as its fundamental law, and subject only to the Ancient Landmarks of Freemasonry to enact laws for its own government and that of its subordinate Lodges. The remaining lodges of other constitutions (two English and one Scottish) may continue to meet in Malta, but new lodges may be founded only by the SGLoM. For months, the representatives of the five founding lodges met and drafted a Book of Constitutions which was adopted at the constituting Grand Lodge Meeting on 18 November 2004.

The first Grand Master of the Sovereign Grand Lodge of Malta was Joseph Cordina. In April 2005, a research lodge was consecrated named Ars Discendi (Art of Learning), and in November 2005 the lodge Flos Mundi (Flower of the World) was consecrated. This latter lodge was intended to attract Maltese and Italian brethren and works in the Italian language. A further new lodge was founded in 2010, named White Sea Lodge. In April 2011 the lodge Mare Nostrum was consecrated taking the number of subordinate lodges to nine.

The Sovereign Grand Lodge of Malta follows the English and Commonwealth pattern of Freemasonry (as opposed to the alternative Scottish Rite, York Rite, and Swedish Rite styles). This means that Malta recognises the three degrees of Craft Freemasonry (Entered Apprentice, Fellow Craft, and Master Mason), plus the Order of Royal Arch Freemasonry, as collectively forming the whole of “pure ancient Freemasonry”. As in England, Royal Arch Chapters may be formed in Malta (with the consent of the Grand Master) and each such Chapter must be attached to a warranted Lodge, and bear the same name and number as that lodge.

The Sovereign Grand Lodge of Malta is recognised by most regular Grand Lodges worldwide.