The debates surrounding the reform of national education in Britain and Ireland in the mid-nineteenth century were often framed as a binary struggle between the religious establishment, which sought to retain control of the national schools, and dissenters who viewed education reform as an important step towards dismantling the state churches' traditional privilege and control over society. In Scotland, however, the picture was somewhat more complicated. While the 1843 Disruption, which split the Church of Scotland in two, was viewed by many within the non-established churches as a victory for dissent, the church that formed out of it -- the Free Kirk -- retained its belief in national and state-supported religion. This establishmentarian stance led the majority of the Free Church to oppose the creation of a non-denominational education system proposed by Scotland's voluntary dissenters, and indeed some within their own church, and especially one which failed to secure a place for religious instruction in the national schools. This article assesses how the fractious ecclesiological context of Scottish Presbyterian dissent influenced the direction of the education debates, particularly over religious instruction, in the almost three decades between the Disruption and the eventual passing of the 1872 Education (Scotland) Act. The education debates tended to reflect broader trends within Scottish dissent after 1843, offering dissenters the opportunity to unite against the weakened establishment in the aftermath of the Disruption, while also highlighting and often exacerbating the ideological divisions which hindered the emergence of a truly unified dissenting movement in Scotland for almost thirty years.