Two raw bentonites, from Argentina (Mt-A) and Turkey (Mt-T), rich in montmorillonite, were loaded with different concentrations of cetylpyridinium chloride (CP), ranging from 50% to 150% of their respective cation exchange capacity (CEC). Their antifungal activity was tested against Alternaria alternata and Chaetomium globosum. Thermal analysis was used to identify the different surface adsorption sites of the CP on the montmorillonite (Mt) samples as well as to quantify the surfactant amount related to each process, which could play a key role in the antifungal capacity of the synthesized materials. Three different CP interaction processes with the Mt surface sites were observed. Two occurring at the outer Mt surface (electrostatic interaction between CP and the negative surface sites of Mt (B), and van der Waals (VdW) interactions between long tails of CP molecules (A) and one at the inner (or interlayer) Mt surface due to the cation exchange between CP and the inorganic interlayer cations (C). The simultaneous occurrence of these processes was confirmed by the increase of the interlayer thickness due to the entrance of CP by C process and the decrease of the initial negative zeta potential values by A and C processes, respectively. The antifungal activity of clays against strains of A. alternata and C. globosum, was evaluated by agar diffusion assay. Then, the inhibition diameter was related to the actual CP load and its distribution according to A, B, and C processes. Samples with the highest inhibition zone, Mt-A-CP150, and Mt-T-CP150, presented the greatest actual CP loaded (103 and 110% CEC, respectively). For both samples, the CP amount related to the A process was the lowest, with values around 10% CEC, while the major contribution occurs for the CP related to the B process (49.9 and 57.7% CEC, respectively). The Pearson correlation coefficients ρ determined between inhibition zone diameters and CP amount related to each adsorption process indicated that the A and B processes play a key role in the controlled release of the CP from the organoclays. For A. alternata the ρ values for A and B processes resulted in 0.84 and 0.87, while for C. globosum 0.84 and 0.91, respectively, being non-significant for C process in both cases.