John Bercow has been addressing a reception for gay newspaper Pink News in parliament.
He said: "We are marking 50 years since the partial decriminalisation of homosexuality.
"There's always a balance to be struck - we don't want to behave as though it's all over, that everything has been done. Nothing remains - because that isn't true.
"I still feel that we can only really have equal marriage when you can b***** well get married in a church if you want to do so."
When the law changed in 2013, churches were offered a protection that they wouldn't be forced to host gay marriages in their building.
Churches wishing to opt-in, can apply to be except from the protection.
Only a small number have chosen to host the ceremonies including the Scottish Episcopal Church and the United Reformed Church.