The data comprise measurements of the 'soluble', 'adsorbed' and 'organically bound' 99Tc concentrations in a diverse set of soils following experimental addition of 99TcO4- and incubation in the laboratory under controlled temperature conditions for 897 days. The long term behaviour of 99Tc in aerobic soils was studied by conducting a laboratory-based experiment in which a set of 20 topsoils from central England with contrasting properties (e.g. pH, organic matter content, land use) were contaminated with 99TcO4- and incubated in the dark, in a moist but aerobic condition, at a temperature of 10 deg C for 2.5 yr. The physico-chemical transformations of 99Tc in each soil microcosm were periodically monitored by means of a three-step sequential extraction procedure conducted on subsamples of incubated soil. The resulting dataset enabled quantification of the kinetics of 99Tc transformation in aerobic soils as a function of soil properties and land uses (arable, grassland and moorland/woodland). The data will be useful in developing models of long-term 99Tc bioavailability in aerobic soils under temperate conditions. Full details about this dataset can be found at https://doi.org/10.5285/4622f906-e28a-4210-aa03-d2e4169b1be8