The effectiveness of modified nanodiamonds (NDs) for the adsorption of mycotoxins, aflatoxin B1 (AfB1) and ochratoxin A (OTA), are investigated in this paper. Binding and release mechanisms of the mycotoxins were addressed using an assortment of NDs modified by different surface treatments, including carboxylation, hydrogenation and hydroxylation, followed by isolating NDs of different sizes. Results indicate that AfB1 adsorption on NDs is directly related to aggregate size, whereas OTA adsorption is primarily centered upon electrostatic interactions that depend on the types of surface functional groups on the ND. Findings show that modified NDs with small aggregation sizes (~40 nm) have greater adsorption capacities for AfB1 than yeast cells walls and untreated NDs from various vendors, but comparable to activated charcoal. In OTA studies, positively charged NDs outperformed clay minerals, which are well-known and efficient sorbents for mycotoxins. Furthermore, ND adsorption capacities can be preserved in a wide range of pH.