Green MSP Patrick Harvie has accused the Scottish Parliament of inviting the head of a "homophobic" US university to address Holyrood.
Cecil Samuelson, president of Brigham Young University in Provo, Utah, led the "time for reflection" session.
Mr Harvie said the institution was run by the Church of Jesus Christ of Latter-day Saints, who believe homosexual behaviour is inappropriate.
Holyrood bosses said speakers were told not to make discriminatory comments.
As part of his address, Mr Samuelson told MSPs: "Our faith and our trust in heaven are strongly linked in our respect and responsibility for all people, including those of vastly different backgrounds or persuasions."
Raising a point of order in the Holyrood chamber after Mr Samuelson spoke, the Green MSP, said: "We've heard today in our time for reflection slot from a speaker who represents an academic institution with a despicable track record of homophobic discrimination.
"This is an institution which is willing to ruin the life chances of young people and to force them to live in fear, simply on the grounds of their sexuality."
But Holyrood presiding officer Tricia Marwick told Mr Harvie: "I would remind you that time for reflection contributors are guests of this parliament and should be shown courtesy by all members.
"I think any member who has heard the speech that Professor Samuelson made today would take absolutely no issue with it whatsoever."
Brigham Young University says it "seeks to develop students of faith, intellect, and character who have the skills and the desire to continue learning and serving others throughout their lives".
The university, established in 1875, says it aims to provide education "in an atmosphere consistent with the ideals and principles of its sponsor", The Church of Jesus Christ of Latter-day Saints, also known as the Mormon Church.
A number of Brigham Young students are working as interns for MSPs.
Business in the Holyrood chamber usually begins with time for reflection, which has featured a range of speakers from different backgrounds.
A Scottish Parliament spokesman said: "A wide range of faith and non-faith speakers have taken part in time for reflection.
"Every speaker is issued with guidance which makes clear all contributions in the chamber must be consistent with the principle of equal opportunities for all and should not include remarks or comments which are discriminatory."