In recent years, there has been a growing interest in plant pigments as readily available nutraceuticals. Photosynthetic pigments, specifically chlorophylls and carotenoids, renowned for their non-toxic antioxidant properties, are increasingly finding applications beyond their health-promoting attributes. Consequently, there is an ongoing need for cost-effective methods of isolation. This study employs a co-precipitation method to synthesize magnetic iron oxide nanoparticles. Scanning electron microscopy (SEM) coupled with energy dispersive spectrometry (EDS) confirms that an aqueous environment and oxidizing conditions yield nanosized iron oxide with particle sizes ranging from 80 to 140 nm. X-ray photoelectron spectroscopy (XPS) spectra indicate the presence of hydrous iron oxide FeO(OH) on the surface of the nanosized iron oxide. The Brunauer–Emmett–Teller (BET) surface area of obtained nanomaterial was 151.4 m2 g−1, with total pore volumes of pores 0.25 cm3 g−1 STP. The material, designated as iron oxide nanoparticles (IONPs), serves as an adsorbent for magnetic solid phase extraction (MSPE) and isolation of photosynthetic pigments (chlorophyll a, lutein) from extracts of higher green plants (Mentha piperita L., Urtica dioica L.). Sorption of chlorophyll a onto the nanoparticles is confirmed using UV–vis spectroscopy, Fourier transform infrared photoacoustic spectroscopy (FT-IR/PAS), and high-performance liquid chromatography (HPLC). Selective sorption of chlorophyll a requires a minimum of 3 g of IONPs per 12 mg of chlorophyll a, with acetone as the solvent, and is dependent on a storage time of 48 h. Extended contact time of IONPs with the acetone extract, i.e., 72 h, ensures the elimination of remaining components except lutein, with a spectral purity of 98%, recovered with over 90% efficiency. The mechanism of chlorophyll removal using IONPs relies on the interaction of the pigment’s carbonyl (C=O) groups with the adsorbent surface hydroxyl (–OH) groups. Based on molecular dynamics (MD) simulations, it has been proven that the selective adsorption of pigments is also influenced by more favorable dispersion interactions between acetone and chlorophyll in comparison with other solutes. An aqueous environment significantly promotes the removal of pigments; however, it results in a complete loss of selectivity.