The supremacy of King William following the battle of the Boyne in 1690 was not as advantageous to the Presbyterians as it might have been because as a constitutional monarch, he could not do all that he wished for them. Thus until his death in 1702, William was only able to influence existing law while the Irish Bishops, who represented about half of the membership of the Irish House of Lords, continued their vindictive actions against Presbyterians. Despite this, by 1702 there were nine Presbyteries under three sub-synods of Belfast, Monaghan and Lagan.

Yet again there was trouble in store as in 1704 the Test Act was introduced, not this time an oath, but a requirement for all appointees to public office to take the Communion in an Episcopal church within three months or lose their position. It is possible that the government thought that they could obtain converts to Episcopacy by this Act but it was not to be.

In Londonderry, 10 of the 12 Aldermen were Presbyterians and lost their office; while 14 of the 24 burgesses were expelled. In Belfast nine of 13 burgesses lost their seats. Over the country generally, public office holders such as magistrates postmaster and town councillors were ejected for their faith.

Other forms of discrimination rained down on the Presybterians, with landlords encouraged to charge Presbyterians higher rents; they were banned from being school teachers, the leases for church lands prohibited letting to a Presbyterian tenant or building of a Presbyterian church, and even in some parts the doors of the churches were nailed shut to prevent services being held.

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