Clay-bacterial interaction can significantly influence the biodegradation of organic contaminants in the environment. A moderate heat treatment of palygorskite could alter the physicochemical properties of the clay mineral and thus support the growth and function of polycyclic aromatic hydrocarbon (PAH)-degrading bacteria. By using ¹⁴C-labelled phenanthrene and a model bacterium Burkholderia sartisoli, we studied the mineralization of phenanthrene on the surface of a moderately heat-treated (up to 400 °C) palygorskite. The heat treatment at 400 °C induced a reduction of binding sites (e.g., by the elimination of organic matter and/or channel shrinkage) in the palygorskite and thus imparted a weaker sequestration of phenanthrene on its surface and within the pores. As a result, a supplement with the thermally modified palygorskite (400 °C) significantly increased (20–30%; p < 0.05) the biomineralization of total phenanthrene in a simulated soil slurry system. These results are highly promising to develop a clay mineral based technology for the bioremediation of PAH contaminants in water and soil environments.