This study aimed to profile the metabolites, piperine content, and biological activities (antioxidant, anti-inflammatory, anticancer, antibacterial, and apoptotic cell) of 15 samples of Piper nigrum L. from various geographic regions of Thailand. UHPLC-QTOF-MS was applied to establish alkaloid profiles of the P. nigrum L. samples. PCA and HCA analysis showed that the samples from the PN-1, PN-2, and PN-11 sources differed significantly from those of other sources in terms of compound type and alkaloid concentration profile. Comparative analysis based on a validated HPLC-DAD method was used for the standardization of 15 varieties of P. nigrum L. with piperine as a standard phytomarker which revealed that PN-4 source possessed a high content of piperine. PN-2 showed the highest antioxidant capacity (DPPH activity) while PN-10, PN-12, and PN-15 showed the highest FRAP activity. PN-11 source showed high inhibition of anti-inflammatory and anticancer properties. Furthermore, PN-3, and PN-4 also showed the highest both anti-inflammatory and antibacterial activity. Almost samples have been shown to induce late apoptosis and necrosis in SW480 cell line. This study will also be useful for the development of quality control parameters through the standardization of varieties of P. nigrum L. as raw materials in traditional medicine formulations. HIGHLIGHTS Metabolite profiling of the nigrum L. varieties from 15 different geographical locations in Thailand Quality control parameter for standardization based on marker analysis by HPLC-DAD using piperine as the marker compound Comparisons of metabolites among 15 different cultivations by Principal Component Analysis (PCA) and hierarchical cluster analysis (HCA) Biological activity of the nigrum L. varieties from 15 different geographical locations in Thailand GRAPHICAL ABSTRACT