Smectites are effective binders of aflatoxin in aqueous solutions. Unfortunately, their efficacy is reduced in guts because of interference by biomolecules and essential nutrients within the gut. Tunnel structures in palygorskite and sepiolite may function as molecular sieves and may, therefore, serve as alternatives or complements to smectites in binding aflatoxins but not larger biological compounds. The objective of the current work was to determine the effect of heat treatment on aflatoxin B1 (AfB1) adsorption and selectivity for biomolecules by two palygorskites (Plg_PK and Plg_CN), sepiolite (Sep), and a palygorskite-smectite mixture (Plg-Sm) in comparison with a smectite (Sm-37GR). The clays were heated at 250, 400, 500, and 600°C while phase and structural changes were characterized by X-ray diffraction and infrared spectroscopy. Comparative AfB1 adsorption was determined in aqueous and in simulated gastric fluids. The clay structures collapsed irreversibly in Sm-37GR and folded in fibrous clays with heating at 400°C or more. Sm-37GR adsorbed more AfB1 than all of the other clays; the estimated adsorption capacity followed the trend Sm-37GR (44 g kg–1) > Plg_PK (18.12 g kg–1) > Sep (12.7 g kg–1) > Plg_CN (11.4 g kg–1) > Plg-Sm (9.0 g kg–1). This trend appeared to be correlated with the abundance of smectite in the clays. Sepiolite had greater binding strength for AfB1 than the other clays. With intact clay structures, heating induced a negligible effect on AfB1 adsorption by the fibrous clays while in Sm-37GR and Plg-Sm, adsorption increased with heating at 250°C. Tunnel folding and structural collapse that had occurred at 400°C caused an abrupt decline in AfB1 adsorption irrespective of the clay type. The sepiolite clay adsorbed the least pepsin (370 g kg–1) while smectite adsorbed the most (1430 g kg–1). Consequently, in the simulated gastric fluid, adsorption declined by 25–30% in sepiolite, 52–60% in smectite, and remained unaffected in the palygorskites. Aflatoxin B1 adsorption probably occurred through H-bonding at the surface with the silanol group in palygorskite and sepiolite. No evidence that AfB1 molecules occupied the tunnels of the natural or heated palygorskite or sepiolite was observed in the present study. Palygorskite and sepiolite had a much smaller adsorption capacity for AfB1 than the smectite but also adsorbed less pepsin; therefore, both may be effective aflatoxin binders in gastrointestinal systems.