More than 1,500 sailors and marines lined the deck of the Portsmouth-based helicopter carrier as she entered the port of Valletta.
As well as an onboard reception for the Earl and Countess of Wessex, the ship will be holding an affiliation event for representatives from the Maltese cities of Senglea, Vittoriosa and L’Isla.
The helicopter carrier is twinned with the three cities due to a previous HMS Illustrious which was bombed during the Second World War and underwent extensive repair at the Grand Harbour in Malta.
Captain Martin Connell, Commanding Officer of HMS Illustrious, said it was a proud moment for him to be sailing HMS Illustrious into Valletta. He said:
We are very much aware of not just the history of this ship but also the previous Illustrious and what the people of Malta did to help save her in 1941.
The Maltese Government also allowed the Grand Harbour in Valletta to be used for berthing by HMS Cumberland and HMS York following their evacuation of British nationals from Libya in 2011.
This time in Grand Harbour, sailors and marines from HMS Illustrious will be helping out with a variety of worthy causes including a clean-up of outdoor spaces in collaboration with the Nature Trust.
Later in the week HMS Illustrious will be joined by the Royal Navy fleet flagship, HMS Bulwark, and Royal Fleet Auxiliary ship Mounts Bay.
HMS Illustrious is part of the Cougar 12 deployment - a three-month work-up of the Royal Navy’s Response Force Task Group (RFTG).
The deployment is a test of the RFTG’s capability should it be called into action at short notice.
The force is designed to respond to rapidly unfolding world events - the last time being Libya in 2011.
As part of Cougar 12, the ships have been working with Royal Marines commando units and the Fleet Air Arm to put their amphibious capability to the test - the power to transfer marines from ships onto the beaches of hostile nations.
As well as exercising the 3,000 British sailors, marines and airmen, the task force has worked alongside French and Albanian forces to ensure the nations could co-operate on a military level in the future.