Tuesday’s vote at the Kirk’s annual gathering in Edinburgh came a month before the UK referendum on EU membership takes place.
The Kirk said the motion to remain was carried with a clear majority stamping their feet at the Assembly Hall on the Mound.
Tuesday’s vote represented the fifth time in the last 20 years that the Assembly has formally supported continuing membership of the EU.
However, its social care council noted that the EU has changed greatly in the past 20 years with public debate focused on a few cental issues such as the free movement of people, the economic cost and benefits of membership, environmental issues and the refugee crisis.
It also informed delegates that the EU was “struggling” to respond to the arrival of the large number of refugees with member states opting out of proposals for a co-ordinated, shared response.
The motion carried by an overwhelming majority of 730 commissioners gave thanks for the work of the EU in promoting peace, security and reconciliation amongst its nations and stated that the UK should remain in the EU.
During a short debate, commissioners heard a range of voices recognising the European Union’s successes.
Rev Aniko Schuetz Bradwell, a minister in East Lothian, said she had grown up in East Germany close by the wall until it was torn down when she was seven.
She said: “We have a choice now and I hope we will choose to build bridges, not to erect another wall.”
But Rev Dr Karen Fenwick, a minister in Angus, said she objected to the Church appearing to tell people how to vote.
She said: “We are not a political party or a trade union. I think the Scottish public are quite capable of knowing we support the EU without us telling them what to do.”
Rev Sally Foster Fulton, Church and Society Convener, welcomed the Assembly’s continued backing for EU membership.
She said: “We are saying as a Church that much has been gained by being a part of the European Union, and we believe there is a great deal we can do in the future as an integral part of Europe.
“We recognise it is not perfect, but the EU is a work in progress and not the finished product. The only way we can continue to be part of the transformation is to remain within it.”
Commissioners also instructed the Church and Society Council, in the event of a decision to remain in the EU, to explore ways of increasing understanding of and engagement with the European Parliament and EU institutions.