Agricultural activities cannot be separated from indigenous knowledge (IK), which has developed and continues to be strongly maintained by Bugis–Makassar farmers in the face of rapidly developing science and technology. The objective of this study was to explore the IK practices in rice cultivation of the Bugis–Makassar farmer community, as well as the process of integrating IK and scientific knowledge into decision making. The study used a number of qualitative methodologies to gather information, including meetings, focus group discussions, in-depth interviews, and semi-structured interviews. Our results show that IK is slowly disappearing and being replaced by middle-aged people and youth, who seem to care more about modernization than assimilation. However, with the existence of Tudang Sipulung, the fading of local wisdom may be inhibited. Tudang Sipulung’s strength lies in the government’s involvement in integrating IK and scientific knowledge into formal forums and agreement. The Tudang Sipulung agreement is formally binding with constitutional sanctions applied. In order to provide optimum benefits, engaging young farmers in the understanding and preservation of indigenous and scientific knowledge is recommended to preserve local culture and transfer modern technology.