Cephalotaxus and Taxus both possess significant medicinal values in the traditional medicine system. Even though the tribal communities in the Himalayas have used these genera extensively, little is known about their ethnopharmacological properties. The study aims to investigate the biochemical profile and biological activities of various extracts of Cephalotaxus and Taxus. This study examined six different accessions of Cephalotaxus and Taxus growing in the northeastern Himalayan region of India for their biochemical components and biological activities. This report considers three species of Cephalotaxus, namely, C. mannii, C. sinensis, and C. griffithii, and one species of Taxus viz. Taxus wallichiana. The stem and leaf extracts of all six selected accessions were biochemically characterized using HPLC/LC–MS. Results have demonstrated the presence of several medicinally important chemicals like harringtonine, rutin, caffeic acid, gallic acid, and a few other biologically active compounds. The isolates were tested for their antibacterial and anti-plasmodial properties. The zone of inhibitions for various extracts ranged from 3–11 mm in the case of Cephalotaxus and 3–6 mm for Taxus. Leaf and stem extracts of all six accessions were found negative for antiplasmodial properties. The data from this study can further serve as a framework for a thorough analysis of various compounds and their antibacterial and antimalarial properties.