Malaysia's furniture manufacturing industry is made up of small and medium enterprises (SMEs), which contribute significantly to the country's economy. One major issue that these SMEs face is sustainable manufacturing: lowering throughputs and increasing production efficiencies. The study aims to improve the efficiency of producing a learning tower; a furniture product by an SME called Industerior Design by implementing material flow analysis (MFA) to monitor production throughputs. The MFA was used to compare two different learning tower designs (Design A and B). The most sustainable design was determined based on the MFA. A cause-and-effect analysis was also carried out using the Ishikawa fishbone diagram to identify potential causes of production inefficiencies. Both designs were proven to have the same processes involved and the same waste stream generated; however, Design A produces four learning towers from a single wood plank with 15.5% waste generated, while Design B produces only two towers with 44.6% waste generated. Of the waste generated by both designs, 60% from Design B was recyclable, while for Design A only 25% was reusable. Inefficiencies can be caused by a lack of skilled workers, a lack of or infrequent maintenance of equipment, or the design of the product itself. When the amount of recyclable waste that can be used for other future projects was considered, it was determined that Design B was more sustainable in the long run. MFA is thus thought to be a simple but powerful tool that can be easily implemented by SMEs in designing out waste from their products as the furniture industry moves toward more sustainable manufacturing and a more circular economy.