From the public entry to the Grand Master's Palace on Triq il-Merkanti it's possible to visit the State Apartments; note that the apartments are closed from time to time when official state visits are taking place. Heritage Malta conducts guided tours (included in the cost of admission) of the apartments.

A staircase past the Armoury entrance provides access to the State Apartments. Only a few rooms are open to the public, depending on what is currently being used. The long Armoury Corridor, decorated with trompe l'oeil painting, scenes of naval battles, blue colours and the portraits and escutcheons of various Grand Masters, leads to the Council Chamber on the left. It is hung with 17th-century Gobelins tapestries gifted to the Order in 1710 by Grand Master Ramon Perellos. They feature exotic scenes of Africa, India, the Caribbean and Brazil, including an elephant beneath a cashew-nut tree; an ostrich, cassowary and flamingo; a rhino and a zebra being attacked by a leopard; and a tableau with palm trees, a tapir, a jaguar and an iguana.

Beyond lie the State Dining Room and the Supreme Council Hall, where the Supreme Council of Order met. It is decorated with a frieze depicting events from the Great Siege of 1565, while the minstrels' gallery bears paintings showing scenes from the Book of Genesis. At the far end of the hall a door gives access to the Hall of the Ambassadors, or Red State Room, where the Grand Master would receive important visitors, and where the Maltese president still receives foreign envoys. It contains portraits of the French kings Louis XIV, Louis XV and Louis XVI, the Russian empress Catherine the Great, and several Grand Masters. The neighbouring Pages' Room, or Yellow State Room (despite the abundance of greenish tones), was used by the Grand Master's 16 attendants, and now serves as a conference room.