Why did the church lose its authority at the end of the Middle Ages?

Firstly, because of hypocrisy, the inappropriateness of one’s own way of life to what they themselves teach, acquisitiveness, careerism within the church organization, neglect of the needs of their parishioners, especially the poor.

Secondly, competing with the secular power, the church inevitably pushed the latter to support anti-church forces, in particular, supporters of the reformation. As a result, they were able to more easily advocate and spread their ideas.