Potentially toxic metals in the urban chemical environment impose risks to both ecosystem and human health. Here, we evaluate the labile pools and availabilities of non-anthropogenic Ni, Cr, Co and Mn in soil samples from Thiva town (central Greece) and investigate their associations with common soil properties and geochemical data obtained by the aqua regia and single selective dissolutions. Experimental work included the initial application of the sequential extraction protocol proposed by the European Community Bureau of Reference and chemical extractions with ethylenediamine tetraacetic acid solution and a modified physiologically based extraction test with the aim to obtain the operationally defined fractions of plant availability and human bioaccessibility, respectively. The leachate results demonstrated that despite the significant contribution of residual metal species especially for Ni and Cr, the studied serpentine soils provide chemically labile pools for all the considered elements. Nickel was found to be the most available metal with the order being Ni > Cr ∼ Co ∼ Mn for plant uptake and Ni > Cr > Co ∼ Mn for human bioaccessibility. The aqua regia extractable concentrations are not predictors of elemental availabilities except for Ni bioaccessible data interpreting however only a moderate percentage of the total variance. The incorporation of basic soil properties (mostly total organic carbon), geochemical data for the major elements Ca, Mg and Fe and ammonium oxalate extractable Cr significantly improved the estimations for individual elements entailing the strong influence of the chemistry and mineralogy of soil materials to the release of focus metals from the soil matrix. This study provides for the first time bioaccessible data for serpentine-derived soils that are more realistic for evaluating potential adverse effects on the human health.