Reverend Yousouf Gooljary has urged the Kirk to mount plaques and educate parishioners about the connections between the slave trade and the buildings where they worship.
The Kirk is due to report on its links to slavery next year.
Dornoch Cathedral in Sutherland has been highlighted as one building that stands, in part, due to such wealth.
It was refurbished in the mid 1830s after a donation of £15,000 from Elizabeth, Countess of Sutherland, a sum which equals some £1.39m at today’s values.
Elizabeth, who also played a key role in the Sutherland Clearances, benefited from the huge wealth of her mother, Mary Maxwell ,who inherited £5,000 from her father whose fortune was made ‘mostly in trade and plantations in Jamaica’.
Rev Gooljary, a minister with the Scottish Episcopal Church and member of the Iona Community, said: “Churches have to acknowledge their links to slavery, we need to have recognition and we need to educate.
“The response from churches has been mixed. At first there is some shock and surprise , some seem a bit lost, so are looking for leadership to help them.
"I think the Church of Scotland should see the issue as giving a lead in a wider one of engaging with a cultural conversation across the whole of Scotland , it’s more than just about their churches .”
He will protest outside the General Assembly of the Church of Scotland next month to raise awareness of the issue.
His campaign also looks at links between slavery and the United Free Church of Scotland, the Scottish Episcopal Church and the Free Church of Scotland.
The links between the cathedral at Iona Abbey and the wealth of its former owners, the Dukes of Argyll, whose fortune was partly derived from the labour of enslaved people, have also been examined.
Cathedral repairs were carried out during the time of William, the 8th Duke of Argyll, whose father’s second and third wives both came from plantation and slave owning families in Virginia and Jamaica.
Rev Gooljary said: “In these ways wealth linked to slavery played a role in the steadying and recovery of the house of Argyll in the second half of the 19th Century, a period which saw, the repair programme which in large part recreated the Abbey as we experience it today.”
The Iona Cathedral Trust will put a motion to the General Assembly which urges the Kirk to support research into its links with slavery and places of worship.
A spokesman for the Church of Scotland said: “The more challenging aspects of our history is something that the Church of Scotland is looking into, and ties in with recent motions from the General Assembly condemning racism as sinful and affirming that black lives matter.
The General Assembly of 2020 instructed its Faith Impact Forum to report on the issue of racial justice and the legacy of slavery and to consult widely with people of colour in the Church of Scotland and with Black Majority churches in Scotland.
It will report in 2023.