Many ancient early diagenetic siderite concretions are thought to have been precipitated by microbially-mediated reactions, and their trace element chemistry has been used to infer palaeoenvironments of formation (e.g. marine versus freshwater). In this study, pure cultures of the microorganism Geobacter metallireducens were used to precipitate siderite in the laboratory at a range of temperatures (18–40°C). Magnesium and calcium, in three different ratios (3:1, as in seawater, 1:1, and 1:3 as in freshwater), or manganese were added to some cultures at each incubation temperature to study trace element incorporation. The siderite produced exhibited the rhombohedral crystal form typical of concretionary siderite. However, this microbial siderite did not simply retain the trace element chemistry of the water from which it precipitated, as is assumed in palaeoenvironmental interpretations. Instead, manganese and calcium incorporation were found to be inversely proportional to the rate of microbial activity, which itself is dependent upon the nutritional status of the microorganisms. Magnesium incorporation was found to be rate-independent, and at high Mg/Ca ratios, it caused inhibition of calcium incorporation. In short, the influence of microorganisms on the trace element composition of early diagenetic siderite must be taken into account in order to produce valid palaeoenvironmental interpretations.