It was 'modernised' in the 1950s to become the school hall, then known as the Oei Tiong Han Hall. All arches were flattened, Doric columns were turned into cylindrical columns and external walls and windows were added to enclose it. This hall was restored to its original state based on an original drawing found on site.

The Glass Hall is commonly used for exhibition openings and related programmes.

All the important elements of the chapel are preserved. These include the small 'basins' for holy water, Stations of the Cross, original pressed steel ceiling and dado panels, and original concrete floor tiles. Salmon is the original colour of the walls. When the school was taken over for the construction of the Museum, several pieces of old floor tiles were found missing. These were reinstated with the new tiles specially manufactured to match the old. A plaque outside the chapel commemorates Brother Michael (1856 –1936) who, as Director of SJI (1900 – 1914) played a major part in the development of the 3 historic buildings that are preserved.

Waterloo Street Wing 

The Straits Settlements Government had made a generous contribution towards the building funds. Originally, this building had a staircase projecting into the courtyard, taking up much courtyard space. It was removed possibly in the 1950s and modern staircases were added to either of the block. These modern staircases greatly marred the beauty of the exterior of the building and were removed as part of the effort to restore Anderson Building into its original splendour.

Queen Street Wing

Built too small and narrow for conversion to museum use, the building had to make way for the current new structure, designed to harmonise in rhythm and composition with the historic building and yet have a contemporary look.