Jeremy Balfour, who was elected to the Scottish Parliament earlier in May, said Ruth Davidson's partnership with Jennifer Wilson would be recognised legally but not in the Bible.
Ms Davidson is one of three openly gay political party leaders in Scotland but she is the only one to profess a Christian faith.
She announced her engagement on Twitter soon after her party became the official opposition at the May 6 poll.
Mr Balfour, worked for the Evangelical Alliance before his election and has spoken out against same sex marriage before.
"The Bible is for me the book that I take guidance from in how I should live my life," he told the Sunday Herald.
"My interpretation of the Bible is that marriage is between a man and a woman. Clearly other people hold different views on that, and clearly other people have different interpretations of that, but my understanding of the Bible is that marriage is between one man and one woman."
He accepted Ms Davison's relationship would be "a true marriage, in that it is a legal thing," but refused to say whether it would be in the eyes of God.
Ms Davidson, who is a member of the Church of Scotland, recently said she believed same sex marriages will be allowed by the Church in her lifetime.
A Church of Scotland spokesman said: "The Church has asked its Theological Forum to report on the theology of same-sex marriage and it is likely that this report will be considered at the General Assembly of 2017.
"It would be premature to try to predict either what the report will say or how the Assembly will decide."