Yacon (Smallanthus sonchifolius (Poepp.) H. Robinson) leaves is traditionally consumed as herbal tea in many countries including Indonesia. This plant’s antidiabetic properties have been extensively researched, but studies on the responsible active compound identification are scarce. Information on the active compounds is critical for the consistency of Yacon herbal tea quality. The aim of this study was to identify α-glucosidase inhibitors in Indonesian Yacon leaves grown in two different locations using FTIR- and LC–MS/MS-based metabolomics in combination with in silico technique. Yacon leaves ethanol (50 and 95%) and water extracts were tested for α-glucosidase inhibitory activity, with the 95% ethanol extract being the most active. Geographical origins were found to have no major impact on the activity. In parallel, chemical profile of Yacon leaves extract was determined using FTIR and LC–MS/MS. Orthogonal Projection to Latent Structure (OPLS) was used to analyze both sets of data. OPLS analysis of FTIR data showed that compounds associated to α-glucosidase inhibitor activity included those with functional groups –OH, stretched CH, carbonyl, and alkene. It was consistent with the result of OPLS analysis of LC–MS/MS data, which revealed that based on their VIP and Y-related coefficient value, nystose, 1-kestose, luteolin-3′-7-di-O-glucoside, and 1,3-O-dicaffeoilquinic acid isomers, strongly linked to Yacon’s α-glucosidase inhibitor activity. In silico study supported these findings, revealing that the four compounds were potent α-glucosidase inhibitors with docking score in the range of ? 100.216 to ? 115.657 kcal/mol, which are similar to acarbose (? 115.774 kcal/mol) as a reference drug.