We reported the systematic review of anti-diabetic herbal medicine from Indonesia by integrating herbal medicine databases and summarized the anti-diabetic compounds in Indonesian plants. We used data sources from Pubmed and local Indonesian databases such as Portal Garuda and Basis Data Tanaman Obat Indonesia (BDTOI) to elucidate anti-diabetic candidate herbal medicine. We found 927 articles (PubMed) and 70 articles (Portal Garuda) based on the criteria of anti-diabetic properties. After thoroughly assessing those publications, 38 articles on controlling blood glucose were identified. Moreover, we utilized ClinicalTrial.gov to map the evidence. Five species (Abelmoschus esculentus, Allium sativum L, Cinnamomum cassia, Citrullus colocynthis, and Punica granatum L) passed the clinical trial, three of which were intended for use in treating other diseases, and eight of which lacked clinical evidence. Additionally, over 30 compounds were elucidating from those herbs, including quercetin and allicin. In conclusion, we successfully retrieved anti-diabetic herbal medicine from Indonesia by integrating public databases. The molecular docking study was employed to predict and optimize the anti-diabetic outcomes.