The influence of open porosity, water absorption capillarity, water vapour permeability, surface roughness, stone pH and chemical composition on stone bioreceptivity to phototrophic microorganisms was assessed by means of a thorough stone characterisation with subsequent artificially inoculation of limestone samples with a multi-species phototrophic culture and placing them inside a growth chamber for 90 days. A principal component analysis and an analysis of variance (ANOVA) were carried out in order to evaluate the direct relationships between stone bioreceptivity and petrophysical properties. From the principal component analysis, two main components were obtained and assigned a petrophysical/photosynthetic biomass meaning. Stone bioreceptivity, quantified by the amount of chlorophyll a and intensity of chlorophyll a fluorescence present on the stone samples after 90 days-incubation, was included in both principal components. The first component was linked to the amount of chlorophyll a and was highly and linearly associated to capillarity and roughness, and less associated with open porosity and water vapour permeability. The second component, linked to the intensity of chlorophyll a fluorescence measured on the stone surfaces, was not linearly associated with the petrophysycal properties, showing the fallibility of this in vivo chlorophyll quantification technique on the estimation of photosynthetic biomass growing on stone materials, particularly when endolithic growth occurs.