Environmental context: Studying the mechanism of binding between metals and natural organic matter is fundamental to understanding the transport and availability of these contaminants in the environment. The influence of sample treatment on the purification of organic matter showed significant differences in the interaction with metals. The results will contribute to improved modelling of metal binding to organic matter in soils, thereby providing a basis for a more realistic risk assessment. We studied the changes in metal binding characteristics of extracted humic acids induced by HF/HCl treatment followed by dialysis, i.e. the last step of the International Humic Substances Society (IHSS) extraction protocol. We performed metal binding experiments with both the alkaline-extracted material (AE) and the fully purified (FP) humic acid using the electrochemical stripping technique (AGNES) and modelled the results using the NICA-Donnan model. The results showed an increase of free Zn, Cd and Pb concentrations of ~1 order of magnitude for the AE compared with the FP. These differences may be mostly explained by the different carbon content (51.3 % FP and 36.5 % AE) associated with an AE/FP carboxyl ratio of 0.5. Simulations using the NICA-Donnan model showed that halving the amount of carboxylic groups (Qmax,1) for the FP reduced this difference to 0.25 log units for Cd and Zn and to 0.15 log unit for Pb. There is a clear need for further research on the differences between purified v. less-disturbed natural organic material, which will contribute to improved modelling of metal binding to organic matter in soils, hence providing a basis for a more realistic risk assessment.