Delegates at the party’s Spring conference in York were warned the party could suffer at May’s local elections if it was seen to be against faith schools which are popular with many parents.
But a call to make it party policy to phase out faith-based selection within six years was overwhelmingly backed.
Former deputy leader Sir Simon Hughes urged activists to take a more moderate approach and back restricting faith schools to offering just half their places based on pupils’ religion.
He said: “Please let us go out and campaign for the education policies that matter most to us all and unite us, against more grammar schoos, for better school funding, for better commitment to technical education.
“Please don’t put us on the back foot in politics locally and nationally by trying to attack the schools that many people love and cherish and adore. Please just think about the reality.”
He added: “In this time of post-Brexit, when many communities are under attack please don’t look as if we as a party are attacking faith communities which are minority faith communities. That would be a dreadful thing to do when they are already filling so insecure.”
Lib Dem education spokesman John Pugh said many faith schools were “inclusive, serve deprived communities, are appreciated by parents, have dedicated staff and are an ingrained part of many communties”.
While the conference voted in favour of scrapping faith-based selection, it blocked attempts to take a stronger line by removing the party’s commitment to supporting faith schools in the state sector.