The couple worshipped at St Paul's Anglican Pro-Cathedral in the capital Valletta while the Duke was serving as a naval officer bteween 1949 and 1951.
St Paul's is looking to raise £2.6 million in order to restore its ceiling, tower and outer stonework.
St Paul's has also issued a prayer which it's been regularly using as it begins its appeal.
It is Malta's only Anglican cathedral, with the island being predominantly Catholic.
Malta has a significant Christian history, with the Apostle Paul remarking in Acts 28 that he was shipwrecked there.
He said of the Maltese people: "The islanders showed us unusual kindness. They built a fire and welcomed us all because it was raining and cold."
Martin Scicluna, part of St Paul's Pro-Cathedral Restoration Committee, told the BBC: "I think the crucial importance of this church is in its contribution to Malta's cultural heritage and one cannot imagine the Valletta skyline without this cathedral, its spire and its tower."
"God our Father, you have given us a fine heritage with which to witness to the saving acts of our Lord Jesus Christ.
"May we use our resources and imagination to Your glory so that our Pro-Cathedral may continue to shine as an icon of faithfulness in these islands under the watchful protection of the Blessed Virgin Mary and St. Paul.