There are six permanent galleries spread over the two levels of the Malay Heritage Centre. These galleries showcase stories and artefacts from both Singapore's national collection as well as contributions from the community. The artefacts support MHC's focus on Kampong Gelam's historical significance as a thriving port town prior to Raffles' arrival in 1819 and serve as evidence of the increasingly urban and cosmopolitan nature of Singapore Malay society.

The first Istana Kampong Gelam was a traditional timber structure built on stilts, and in honour of the istana's original layout, visitors will commence their tour of the permanent galleries from the upper level and end their visit on the ground level. In the traditional layout, the upper level is called the panggung which serves as the main living and sleeping quarters of the house, while the kolong at the ground level is typically used as storage, work or service areas, and even as a children's play area.