Ginkgolic acids (GAs; anacardic acids; 6-alkylsalicylic acids) are both unwanted constituents in standardized Ginkgo biloba (Ginkgo) extracts and desirable constituents for pharmacological assays. Thus, for the quality control of Ginkgo extracts, the availability of pure GAs is important. In this investigation, inexpensive and easily prepared Fe3O4 magnetic nanoparticles (MNPs) in methanol were used to selectively adsorb GAs from crude petroleum ether extracts of Ginkgo leaves in the presence of various lipids including other alkylphenols (cardanols and cardols). The adsorption capacity of the MNPs is high, at 4-5% (w/w). The moiety responsible for the adsorption is the salicylic acid group, which binds strongly to Fe(III). Desorption with acidified methanol gave an extract with a GA content of 73%. This could be further separated by preparative HPLC on a C8 column. In total, eight different GAs were captured by MNPs. The MNP adsorption step can replace more traditional column chromatography and liquid-liquid extraction steps and is superior in terms of solvent consumption, selectivity, labor, and energy consumption. MNPs might become an efficient separation technique for selected high-value phytochemicals that contain a salicylic acid moiety.