The day-long event in Windsor Baptist Church in Belfast was organised by the True Freedom Trust.
Demonstrators held a peaceful picket outside the church, branding the conference a form of gay conversion therapy. But the True Freedom Trust said the protesters had misunderstood its message.
It insisted it did not provide therapy or counselling, rather "pastoral support" for Christians who find themselves attracted to members of the same sex but who want to adhere to the Biblical definition of sex as between a married man and woman.
Around 25 to 30 people gathered outside the church in south Belfast on Saturday morning to highlight their opposition. They waved rainbow flags and held placards proclaiming that "love needs no cure".
The demonstration was largely silent, with no songs, chants or speeches. A number of police officers maintained a low key presence, monitoring the event from the other side of the road.
Director of the True Freedom Trust, Stuart Parker
The protest was organised by LGBT health advocacy group the Rainbow Project.
Rainbow Project director John O'Doherty said the conference was engaging in "quackery".
"The True Freedom Trust is a reparative therapy organisation that believe that there is something wrong with being gay and people should move away from being gay," he said.
"We will always stand opposed to this type of quackery in Belfast, we will always protest these events.
"The actions of all reparative therapy and conversion therapy groups are the same - they believe that there's something wrong with being gay and they seek to support people in moving away from being LGBT.
"We don't believe that's the case, we believe that sharing that message is homophobic, we believe that the sharing of that message - particularly within faith groups - has caused huge harm to our community, including substantial loss of life [through suicide].
"We will always stand opposed to it because this message is harmful to our community and LGBT people deserve to know that they are equal to anybody else within society and their identity is something to be celebrated, not something to be shameful of."
The Belfast conference is one of a series being held by the True Freedom Trust across the UK. In promotional literature, the trust said the event was "aimed at Christians who experience same-sex temptations".
Stuart Parker, the director of True Freedom Trust, said he respected the protesters' right to disagree, but he urged respect for his right to hold to his Christian beliefs.
"The True Freedom Trust is an organisation for Christians, we have been going since 1977, and we seek to encourage those, particularly those who have same-sex attractions and believe in an orthodox understanding of what the Bible says about sexuality, just seek to encourage them in their faith and their walk with God," he said.
"It's very clear in our policies and on our website that we don't point people toward conversion therapy, we are not a therapeutic organisation. We are a pastoral ministry, so we look to point people to what the Bible says, to encourage people in their Christian walk.
"We might point people towards a good quality counsellor but not one who wants to direct people to a certain outcome, so we just encourage good quality ethical counselling, but we are not a counselling organisation ourselves."
He added: "Our interpretation of the Bible, which is the mainstream orthodox position of the church in the UK, is that sexual behaviour, God has made it for the marriage for a man and a woman.
"That is the traditional orthodox position and that's what we would encourage people to believe. We are not out there to change other people's minds, we are just here to support and minister to those people who agree with that position."
Asked what message he had for the LGBT protesters, Mr Parker said: "They are very welcome to believe what they want to believe but I think they have misunderstood what we are about - we are not a therapeutic or counselling organisation, we are not here to push our views on other people who disagree with them.
"We respect other people's right to believe whatever they want, we just ask that they would respect our right to hold to an orthodox position on the Bible."
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