It is not yet clear exactly when the CLC (Christian Literature Crusade) store on Castle Street will shut.
Shop manager Pam Kerr told the Inverness Courier of her disappointment of the decision but CLC products will continue to be available to purchase online.
She said: "It's sad because as well as being a valuable resource centre for the Christian community it was a very popular place for people to come in for a coffee and to enjoy some fellowship.
"As well as providing resources for local churches and the Christian community, we supply to places like Wick, Thurso, Ullapool and Skye."
The announcement comes weeks after CLC - one of the country's leading Christian bookstore chains - announced the closure of its branch in Ipswich, Suffolk.
During recent years, numerous bricks-and-mortar Christian bookshops across the UK have closed. The Wesley Own chain closes its last physical branches in 2014.
At the same time, sales of digital books (e-books) have risen. Audiobooks have also risen in popularity.
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