Before the present building went up, a penal chapel stood on the same ground, one of the modest, often makeshift structures that Catholic communities erected during the Penal Laws era, when public Catholic worship was severely restricted and open church-building was effectively forbidden. These chapels were rarely grand, and most have vanished without trace.

The Killaloe chapel is thought to date from the late seventeenth or eighteenth century, placing it squarely within the long period when Catholic practice in Ireland operated under legal constraint. The local historian William Carrigan, writing in 1905, recorded its existence and noted that it sat across the road from the old graveyard. It survived long enough to see the legal climate shift entirely, but not long enough to see the century out. In 1859 it was taken down to make way for the construction of the current Roman Catholic church, which now occupies the same site. The earlier building left no standing fabric, absorbed almost without remark into the ground on which its successor was built.