As well as being famed as a defender of Reformed theology and Covenanter politics, Rutherford distinguished himself as one of the foremost champions of divine-right Presbyterianism. Indeed, so convinced was he of the value and necessity of correct ecclesiastical forms that he published almost three thousand pages on the doctrine of the church and its relationship to the state. In addition, for four years in the mid-1640s he was an active participant in the Westminster Assembly debates on church government, discipline and liturgy.

Rutherford's zeal for ecclesiastical form has puzzled many of his admirers. Generations of Evangelical pietists could hardly comprehend how someone who wrote the warmest of devotional prose could also engage in bitter and labyrinthine polemics against other Protestant believers. What they failed to recognise was Rutherford's conviction that true religion was not simply a matter of passionate subjectivity. For him, it also involved following biblically prescribed forms of church government. This belief set him apart from those like Hooker, who felt that ecclesiastical forms were largely adiaphora – things that were ‘indifferent’ because not prescribed by Scripture, and hence capable of being determined by the magistrate. It also distinguished him from antiformalists like Cromwell, who believed that ecclesiastical and, to some extent, even doctrinal forms were unimportant and that what mattered was the ‘spirit’, the religion of the heart.