Sago industry is an important industry in East Malaysia (mainly Sarawak). Sago starch is produced as an alternative carbohydrate source in the food chain. To produce one tonne of sago starch, a minimum of 20 tonnes of sago wastewater would be generated. In order to comply with local regulation and to reduce environmental impacts, the produced wastewater requires proper wastewater treatment (WWT). However, with several WWT technologies available in the market, this becomes a challenge for decision makers to select WWT technologies with minimum investment cost while meeting discharge regulations. As shown in the previous research works, the investment cost can be minimised by reducing the resources used. This can be done by reused and recycled the treated water within the processes. Apart from this, the cost for waste (sludge cake) generation should be minimised since the sludge cake will not bring any value to the WWT plant. This can be addressed by using the concept of Material Flow Cost Accounting (MFCA). MFCA is a management tool which quantifies material flows across a production process in both physical and monetary values. The application of MFCA had been adapted in previous research works to prioritise waste streams for waste recovery and to reduce investment costs for WWT plants. In this work, MFCA is further extended to a more comprehensive and realistic WWT plant optimisation, taking into account of sludge treatment. The proposed MFCA can determine the monetary value associated with sludge cake production within the WWT plant. To illustrate the proposed approach, a sago-based WWT plant is solved in this work.