In the soil environment, iron oxides co-occur commonly with different types of organic constituents to produce iron oxide–organic composites that play an important role in the biogeochemical cycling of trace metals. We investigated copper (C u) adsorption on synthetic goethite, P seudomonas putida (CCTCC M209319) bacterial cells, humic acid (HA) and their binary and ternary composites with batch adsorption experiments coupled with isothermal titration calorimetry (ITC). Morphological characterizations show that the three components can form closely combined and heterogeneous aggregates with one another. The kinetics of sorption of C u to these composite materials conforms to the pseudo-second-order model, whereas the C u sorptivities deviate from linear additivity. Specifically, C u sorptivities on the binary goethite– P. putida and P. putida – HA and ternary goethite– P. putida – HA composites are less than expected assuming additivity, whereas the opposite is seen for the binary goethite– HA composite. There is considerable masking of adsorption sites in the ternary goethite– P. putida – HA system, but the binding sites on bacteria are not completely covered, as shown by the adsorption enthalpy and entropy (19.60 kJ mol−1 and 120.9 J mol−1 K−1, respectively) for the ternary composite. We conclude that the binding affinity of C u for the binary goethite–humic acid composite is larger than that for the bacterial composites with goethite or humic acid, or both. This research indicates that bacteria, iron oxide and humic substances exhibit different behaviour in the sequestration of heavy metals when they form various binary and ternary complexes in natural environments.