A comprehensive study was conducted toward the green and facile synthesis of biocompatible magnetite nano particles for the efficient removal of organic contaminants from water. The nanoparticles were synthesized using a modified co-precipitation method and functionalized by the taxane diterpenoids extracted from Taxus baccata L., and fully characterized using UV-vis spectroscopy, SEM, FTIR, VSM, and XRD. The synthesized monodisperse magnetite nanoparticles, with a narrow size distribution of less than 50 nm, displayed significant and stable magnetic activity without surface oxidation after several months. The batch experiments clearly indicated the efficient iron-catalyzed removal of Nile blue, methylene blue, methylene orange, and 4-nitrophenol for several cycles without significant loss of catalytic activity. The relevant kinetic data of the dyes removal reactions were fitted to a pseudo-first order model. Moreover, in vitro MTT assay revealed high biocompatibility of the nanoparticles with no significant toxicity on different human cell lines. The overall results indicated high potential of green synthesized, biocompatible magnetite nanoparticles for the environmental applications especially wastewater remediation.