The site of Istana Kampong Glam was excavated in early 2000 and excavations have continued sporadically until mid-2003. 12 squares have been excavated on the site. All squares were excavated till sterile layer was reached at the depth of 80-90cm.

Istana Kampong Glam is a 19th and 20th century site. The present Istana was built around 1842 but written accounts have described a wooden structure that Sultan Hussein and his family lived in as early as 1830. Investigations on the Southeast corner of the site have pointed to a structure that might possibly predate the Istana.

The earliest dated artifacts were VOC (Dutch East Indies Company) and mid-Qing coins. Other artifacts recovered were mostly from the 19th and 20th century and consisted of locally made Malay earthenware; European transfer print ceramic and modern porcelain wares; local and imported glassware; Chinese exported and locally made porcelain and stoneware; Japanese ceramic ware; metallic tools; metal slag; terrestrial and marine faunal bones as well as various species of marine gastropods and bivalves among others.