The new Custom House was unpopular with the Dublin Corporation and some city merchants who complained that it moved the axis of the city, would leave little room for shipping, and was being built on what at the time was a swamp and is detailed as reclaimed land on John Roque's 1756 map of Dublin as being part of Amory's Grant.

Purchase of land was delayed and proved exorbitant and the laying of foundations was disrupted by the High Sheriff and members of the Dublin Corporation with a mob of several thousand.

[1] The adjacent original Custom House Dock and swing bridge on the East side of the building were also designed by Gandon and completed slightly later in 1796.

As the port of Dublin moved further downriver, the building's original use for collecting customs duties became obsolete, and it was used as the headquarters of the Local Government Board for Ireland.

The results of this reconstruction can still be seen on the building's exterior today – the dome was rebuilt using Irish Ardbraccan limestone which is noticeably darker than the Portland stone used in the original construction.