Greg Mulholland, MP for Leeds North West, said Liberal Democrat MPs who voted against the recent gay marriage legislation had been "pilloried" by colleagues.
Mr Mulholland, who abstained during the second reading of the bill and put forward amendments to the proposed law, said: "Freedom of conscience seemed to be pushed out of the debate."
Two Liberal Democrat MPs - Sarah Teather and John Pugh who are both Catholic - voted against the same-sex marriage bill.
In his contribution to a new collection of essays by Christian Liberal Democrats, Liberal Democrats Do God, published by the Liberal Democrat Christian Forum, Mr Mulholland argued that religious views were being increasingly seen as unwelcome within the party.