The 89-year-old British monarch praised the accomplishments of the 53-nation Commonwealth and her happy associations with Malta.
"Prince Philip and I first came to live here in Malta in 1949, the year the Commonwealth was founded," she said, hailing a vast advancement in freedom and human rights in the decades since then. "I have been privileged to witness this transformation and to consider its purpose."
Between 1949 and 1951, Philip was stationed on Malta as a Royal Navy officer and the future queen lived as a military wife, rather than a duty-burdened heir to the throne.
The Commonwealth links more than 2 billion people on five continents, including large countries like India, Australia and Canada and small island states like Tonga and Vanuatu.
The leaders Friday elected Baroness Patricia Scotland of Britain as the new secretary general. She will take office in April, 2016 and become the first woman to fill the post.
She was accompanied to Malta by her husband Prince Philip, her son Prince Charles, the heir to the throne, and Charles' wife, Camilla.
The queen paid tribute to Philip, praising his "boundless energy and commitment" to the Commonwealth, and to Prince Charles and his wife Camilla who also came to the conference.
French President Francois Hollande plans to address Commonwealth leaders later Friday ahead of the U.N. climate change conference beginning in Paris next week.
British Prime Minister David Cameron, meanwhile, has announced plans to set up a Commonwealth unit targeting the extremist "scourge."
Maltese Prime Minister Joseph Muscat said the Commonwealth needs to become more relevant to the aspirations of its citizens.
"The Commonwealth must have an agenda with clear priorities, especially in the fight against radicalization and the tackling of the migration phenomenon, which can be challenged through education and employment," Muscat said.
"Terrorists are more scared of well-educated girls and boys who manage to get a good job than they will ever be of any army," he said.