Abstract Ancient and modern stromatolites are potentially a challenge for petrophysicists when characterizing biosediments of microbial origin. Because of the heterogeneity, sometimes very cemented and lacking porosity, sometimes highly porous, these widely differing states can be used to develop techniques that can have wider application to addressing the representative elementary volume (REV – single or multiple REVs) challenge in microbial carbonates. Effective media properties – like porosity – need to be defined on REV scales and the challenge is that this scale is often close to or significantly larger than the traditional core plugs on which properties are traditionally measured. A combination of outcrop images, image analysis techniques, micro-computed tomography (CT) and modelling have been used to capture the porosity (or in some cases, precursor porosity) architecture and provide a framework for estimating petrophysical property sensitivities in a range of situations that can be subjected to further calibration by measurements in relevant microbial reservoir rocks. This work will help guide the sampling approach along with the interpretation and use of petrophysical measurements from microbial carbonates. The bioarchitectural component, when controlling porosity in microbial carbonates, presents a significant challenge as the REV scale is often much larger than core plugs, requiring careful screening of existing data and measurement and additional geostatistical model-based approaches (with further calibration).