The couple, who will later fly to Cuba, have been touring five Commonwealth Caribbean realms and were greeted by Bishop Michael Maxwell of the Anglican Diocese of Barbados.
Charles shared a few words with Bishop Maxwell before a fanfare announced the arrival of the royals to the parishioners sitting in the pews.
The prince and duchess were joined by a number of their entourage who sat in the seats behind the couple.
The service was staged for Charles and Camilla, who were featured in the prayers as were the Queen and Duke of Edinburgh.
Bishop Maxwell asked God to "endue them with thy Holy Spirit, enrich them with thy heavenly grace, prosper them with all happiness and bring them to thine everlasting kingdom..."
Charles and Camilla were bid farewell from Barbados by a ceremonial guard of honour.
The prince acknowledged the troops formed in three lines in front of him and stood still as the national anthem was played.
The couple then walked up the stairs of RAF Voyager before heading inside.
Meanwhile, the British Embassy in Havana has described the royal visit to Cuba as "a historic moment".
It tweeted: "Everything is ready for today when TRHs The Prince of Wales and The Duchess of Cornwall arrive in #Cuba for the first official #RoyalVisitCuba.
"A historic moment for both countries."
The Prince of Wales and Duchess of Cornwall have arrived in Cuba for a four-day visit - a first by members of the royal family.
Charles has laid a wreath at a monument in Havana erected in memory of Cuba's national hero Jose Marti, an essayist and poet.
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