Following water penetration of the south wall, gallery staircase and roof in 1993, an architectural study revealed the need for a comprehensive programme of restoration upon a building so well-constructed that only modest maintenance had been required for over a century.

An Appeal Fund was established and launched with a series of fund-raising concerts by Bryn Terfel, Morriston Orpheus Choir and other leading Welsh singers and choirs who have regularly performed in the Tabernacle. Support was given by local businesses, notably by the Julian Hodge Foundation, by CADW and the Welsh Government.

The work has been undertaken in three main stages:

1. 1995-1997. Re-roofing, restoration of main facade including reconstruction of Corinthian column-heads, repointing and internal decoration of south wall and staircases. Manufacture and installation of cast-iron drainpipes and hopper-boxes to match the original 1872 design.
2. 1997 – 1998. Restoration of the 1922 Hill Norman & Beard three-manual organ by Harrison & Harrison of Durham. Renewal of pneumatic tubing, releathering of motors, cleaning of all 2407 pipes, removal and reconstruction of console at the Durham works. The organ is an unchanged example of an Edwardian concert instrument; following the restoration it was accorded a Historic Organ Certificate by the British Institute of Organ Studies.
3. 2010 – 2012. Restoration of the 120ft high east elevation, including stonework, windows and stained glass. Pointing of spire and renewal of capstone and bellframe, updating of electrical installation throughout the building and lightning conductor to current regulations.

The congregation and the community have raised £603,000, ie 60% of the cost, CADW grants supporting the remainder.