In 1989 the right wing and lateral parapet statues of della Quercia's fountain were the first to be dismantled and removed from the loggia of the Palazzo Pubblico; this was followed in 1995 by the left wing and in 2000 by the remaining central section (rear wall) of the fountain. Once free from the surrounding structure each piece was wrapped in white packing foam and crated for transport. Some of the pieces were wrapped in ‘bandages’ and, where necessary, plaster was applied to fractured areas on site before transport. In order to lower the crates to street level (some 50 metres below) a large crane was parked in the Piazza del Mercato, the square located behind the Palazzo Pubblico directly under the loggia. The crates were then transported at first to the Opificio delle Pietre Dure's laboratory in Florence, and in 2000, directly to the laboratory of Santa Maria della Scala in Siena.

The lateral parapet statues (identified in the documents pertaining to the restoration as Acca Larentia and Rhea Silvia) and the right wing composed of the panels representing Temperance, Faith, and the Expulsion of Adam and Eve were cleaned first (our phase one), using a chemical process. In order to remove the black and dark grey layers, known as the crosta nera, a solution made with ammonium carbonate was used to clean the marble's surface. The amount of ammonium carbonate used in the solution varied considerably (from 5 to 20 per cent) depending on the area treated. A higher percentage of ammonium carbonate was used where the encrustation was thicker and, since this varied, each area had to be evaluated separately. The process entailed covering the marble with wet packs impregnated with the ammonium carbonate solution, thus allowing the chemical to act on the surface. The period of time that the packs were left on the marbles was another variable determined case by case by the restorer.

In the early 1990s, ammonium carbonate was employed more often to clean stone, and while it continues to be used today on specific projects, it was not a particularly good choice for the Fonte Gaia sculptures. The problems evinced with this treatment concerned troubles in controlling the level of cleaning.