The town appears to have been deliberately planted in the mid-seventeenth century by James Harrison, a colonel in Cromwell's army, as a settlement for former Cromwellian soldiers, one of many such planned communities established across Ireland in the wake of the Cromwellian conquest.

The site Harrison chose was not entirely blank. By the time he arrived, there was already a tower house standing here, one of the compact, fortified stone residences that Irish and Anglo-Norman landowners had been building since the medieval period. That tower house was already described as a ruinous castle and bawn in the Civil Survey of 1654 to 1656, when it was recorded as the property of a Charles Carroll. A bawn, in this context, refers to the defensive walled enclosure that typically surrounded a tower house, used to protect livestock and provide a first line of defence. Rather than clear the ruin away, Harrison built his own dwelling directly onto the existing structure. Within a little over a decade, the picture had shifted again: by around 1668, Cloughjordan appears among the recorded possessions of Viscount Dongan of Clane, suggesting the kind of rapid transfer of land and status that was common in the unsettled decades following the Cromwellian settlement of Ireland.