Spurgeon's College made the announcement last month that some students would not be able to access funds from the Student Loans Company.
The Office for Students (OfS) turned down the college's registration application, after it failed its financial sustainability test.
Trustees of the Baptist Union decided to set aside £200,000 to replace Student Loans and Grants that would have been available to Spurgeon's College students.
Baptist Union spokesperson Richard Wilson, told Premier they wanted to ensure those training to be ministers didn't have their studies interrupted.
He said: "We were very worried about the decision that had been made by the OfS and the implication for students who were planning to start their courses this September.
"We're very anxious that college students, Baptist union ministerial students, shouldn't be disadvantaged by this difficult situation.
"We're very keen to see new ministers going through training and fulfilling their calling.
He went on to say that the training of new ministers was essential for the health of the Church.
"We're seeing, like all denominations, a number of our ministers are coming towards retirement. And so we are seeing our pool of ministers declining, we want to be refreshing that with new ministers coming through training,
"We all know that good leadership is essential to churches. So it was not a difficult decision to step in."
Spurgeon College and the Baptist Union have begun work to allocate the funds to 13 students to cover the loans and grants that they would otherwise have received from the government.
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