The mobility and fate of heavy metals in soil depend strongly on their interactions with naturally occurring ligands and sorbents such as bacteria–mineral complexes, which are among the most important bioactive components in soil. However, the mechanism through which the various ligands affect heavy metal adsorption on bacteria–mineral complexes remains unclear. In this study, the effects of several inorganic and organic ligands on Cd adsorption on Pseudomonas putida–montmorillonite (Mont) and Pseudomonas putida–goethite mixtures were examined with measurements of macroscopic sorption. The results showed that citrate and humic acid enhanced Cd adsorption on P. putida–Mont and P. putida–goethite. Conversely, oxalate suppressed Cd adsorption. Phosphate showed both limited and increased Cd adsorption, depending on the types of mixture. Cadmium adsorption was increased on P. putida–goethite, but was reduced on P. putida–Mont. This study provided the first compelling evidence that the effects of ligands on bacteria–mineral mixtures cannot simply be inferred from the effects on the individual components of such mixtures. The positive, neutral or negative effects also depend on the types and concentrations of ligands as well as the mineral species that form the bacteria–mineral mixtures.