The ambiguity inherent in the Toleration Act was particularly visible in the controversies surrounding education. Since 1662 Dissenters had been educated, despite legal restrictions, outside of the Church-controlled grammar schools and universities, but the Toleration Act fundamentally confused matters. Was unlicensed education, at least for Dissenters, no longer illegal under canon and criminal law? Dissenters pushed at the limits of their ambiguous toleration, while clergy and their allies attempted to uphold what they still regarded as a Church monopoly. Dissenters were sometimes shielded from harassment by combinations of local sympathy or pragmatic tolerance, protection by elites, and the effects of the ongoing jurisdictional struggle between the ecclesiastical and secular courts. Disputes came to centre on the university-level ‘academies’ instructing future generations of Dissenting pastors, which promised – or threatened, depending upon perspective – to embed tolerated Dissent permanently in English society. During Queen Anne's reign Dissenting education came under sustained polemical and political assault, culminating in the 1714 Schism Act which confirmed its illegality. This legislative intervention would be overturned in 1719 following the Hanoverian succession, but the disputes about education after 1689 illustrate the profoundly unsettled nature of the post- Revolution religious landscape.

The existing literature on Dissenting education before and after the Toleration Act is in many ways problematic. It has generally displayed a dominating preoccupation with the university-level academies and in particular their curricula and teaching methodologies. Very little research has been conducted on grammar school-level learning outside the oversight of the Church. Stereotyped contrasts with the contemporary universities, supposedly notorious for intellectual lethargy, have been increasingly challenged, but the representation of the academies as a crucible of innovative, ‘modern’ education dominates what are still standard texts. Recent specialised studies, while eschewing progressive teleologies, have not entirely escaped this focus on content rather than context. However, new approaches emphasising the lives of educators and students have done much to revise previously misleading impressions of size, complexity, and stability in the later seventeenth century. With the notable exception of the work of David Wykes, the literature hardly addresses how it was the ambiguities of the Toleration Act which fuelled bitter controversies about education.