In this work, indigenous knowledge of Indonesian medicinal plants and their preparation for traditional medicines in Semarang Regency, Central Java, Indonesia, is investigated. This indigenous knowledge was incorporated into STEM-based teaching/learning as a meaningful aspect of science education in Indonesia. This indigenous knowledge was also scientifically correlated and its integration into STEM-based learning was evaluated. Field visits involving traditional medicine sellers and makers were conducted to gather information on Indonesian traditional medicines. A semi-structured interview technique was used. In addition, field observations were conducted to observe the process of preparing traditional medicines, along with literature studies on their ingredients and benefits. Twenty species of medicinal plants commonly used as herbs were investigated. The STEM approach was used descriptively in the data analysis. Comparative analysis was performed to investigate the relationship between STEM and indigenous knowledge of Indonesian traditional medicines. The correlation between the original knowledge in the community and scientific knowledge in the literature was analyzed to integrate this indigenous knowledge into STEM education and therefore to re-design the experiences in the teaching/learning process. This study showed that scientific concepts in the preparation of traditional medicines have important implications for indigenizing the science curriculum in Indonesia through an ethno-STEM-oriented teaching/learning approach.