The characteristics and mechanisms of competitive adsorption of trace metals on bacteria-associated clay mineral composites have never been studied, despite their being among the most common organic–mineral complexes in geological systems. Herein, competitive adsorption of Pb and Cd on Pseudomonas putida–montmorillonite composite was investigated through adsorption–desorption experiment, isothermal titration calorimetry (ITC), and synchrotron micro X-ray fluorescence (μ-XRF). From the experiment, stronger competition was observed on clay mineral than on bacteria–clay composite because more non-specific sites accounted for heavy metal adsorption on clay mineral surface at the studied pH 5. Both competing heavy metals tended to react with bacterial fractions in the composite, which was verified by the higher correlation of Cd (and Pb) with Zn (R2 = 0.41) elemental distribution than with Si (R2 = 0.10). ITC results showed that competitive adsorption exhibited a lower entropy change (ΔS) at the metal-sorbent interfaces compared with single-metal adsorption, revealing that Cd and Pb are bound to the same types of adsorption sites on the sorbent. The competitive effect on bacteria–clay composite was found to be helpful for a better understanding on the fixation, remobilization and subsequent migration of heavy metals in multi-metal contaminated environments.