This study investigates the synthesis of iron-based nanoparticles (Fe NPs) using pomegranate leaf extracts and their application in removing indole, a persistent organic pollutant commonly found in wastewater. The physicochemical properties of the synthesized Fe NPs and the active biomolecules in the pomegranate leaf extracts were comprehensively characterized. Scanning Electron Microscopy (SEM) and Transmission Electron Microscopy (TEM) analyses revealed that the Fe NPs exhibited quasi-spherical shapes, with sizes ranging from 75 to 105 nm. Energy-Dispersive X-ray Spectroscopy (EDS) confirmed a homogeneous distribution of elements, including C, O, Fe, and S, on the nanoparticle surfaces, with weight percentages of 43.59%, 42.95%, 12.58%, and 0.88%, respectively. Fourier-transform infrared spectroscopy (FTIR) identified key functional groups like −OH, −COOH, and −C=O, which are essential for the capping and stabilization of the nanoparticles. Biomolecules such as ellagic acid (C14H6O8) and gallic acid (C7H6O5) functioned as reducing agents, improving nanoparticle dispersion and preventing aggregation. The synthesized Fe NPs quickly achieved 45.5% removal of indole within just 20 min and maintained a stable removal efficiency of approximately 51.4% after 90 min. This performance was attributed to the synergetic interaction between the biomolecules and the nanoparticles, with the monolayer adsorption of indole molecules on the Fe NP surfaces likely setting an upper limit on the maximum achievable removal efficiency. It appears from this study that pomegranate leaf extracts can be effectively utilized to synthesize Fe NPs as a novel and eco-friendly approach, demonstrating promising potential for the rapid removal of indole from aqueous solutions.