Ginger (Zingiber officinale) and meniran (Phyllanthus niruri L.) is a cultural heritage in Madura ethnic, Indonesia. Madurese herbs were traditionally boiled using pottery which is made from clay. Clay consists of Silica (SiO2), Aluminum silicate (Al2O3), Magnesium (MgO), Calcium (CaO),) Iron (Fe2O3) and Potassium (K2O). This component contributes to the efficacy of traditional Madurese herbal medicine by forming bioinorganic complex compounds. The present study aimed to characterize the bioinorganic complex compounds from Madurese herbal medicine and predict their pharmacokinetics activity. Madurese traditional herbal medicine composition was determined using Liquid Chromatography-Mass Spectrometry/Mass Spectrometry (LC-MS/MS). Then, Fourier-Transform Infrared Spectroscopy (FITR), X-Ray Fluorescence (XRF), Scanning Electron Microscopy (SEM) and X-Ray Diffraction (XRD) analysis were used to determine the functional group, transition metal composition, morphology, and the crystal structure of bioinorganic complex compounds from Madurese traditional herbal medicine, respectively. The pharmacokinetic activity was predicted using ADMET software. The results showed that Fe and Mn bind to hydroxyl groups (-OH) in the 6-gingerol and shogaol compounds to form bioinorganic complex compounds. The morphological structure of Madurese herbal powder was porous slabs. The crystal structures of Madurese herbal powder were amorphous and uniform in size. The pharmacokinetic activity analysis showed that Madura traditional herbal has a high solubility in water and easily absorbed by the body. In conclusion, bioinorganic complex compounds of Madurese traditional herbal medicine can be considered as a therapeutic agent in further research.