Aihtsham Rashid, 39, a businessman from Leeds, led a fundraising drive for the mosque, which in a day alone surpassed its £50,000 target by raising more than £63,000 through donations from across the world.
The Presbyterian Free Church - the local arm of the Free Church of Scotland (Continuing), had called on its followers to pray about the "most unwelcome development".
In a press release, the church stated: "Our main concern is with the religion of Islam itself. If a mosque ever opens, Islam will be able to promote itself in our midst through public worship, despite its beliefs and practices being alien to the religious convictions of the vast majority of our community.
"Islam is wholly inconsistent with the teaching of the Word of God in Holy Scripture, which is the only rule to direct us. It is opposed to the Christian religion as confessed by the Church historically since apostolic times, and as established by law in our land since the Reformation."
The church also raised concerns that "jihadists have entered European countries under the guise of being refugees and migrants, when their real intention has been to wage war on the West on behalf of their religion" as another reason for opposing the mosque being built.
However, it clarified that it had "nothing against individual Muslims, least of all any who have been forced to flee their homelands because of persecution and suffering".
The small island north of Scotland has just over 8,000 people residing there with a very small Muslim community, including a growing number of Syrian refugees.
In his crowdfunding page, Rashid said he had been contacted by the Syrian community on the Isle of Lewis asking for his help to get a mosque to attend.
Urging Christians to pray, the church's statement concluded: "Finally, we urge the Lord's people to make this situation a matter of earnest prayer, asking the Almighty that in His kindness He will grant that no mosque will ever appear in Stornoway. Man may propose, but God always disposes."
The derelict building in Stornoway on the Isle of Lewis has already been granted planning permission and will be available in time for the start of the Islamic month of Ramadan in May.
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