A wide spectrum of tomographic techniques now exists for studying palaeontological specimens, but the suitability of these methods for assessing Earth's oldest prokaryotic life has not been comprehensively investigated. We evaluated the ability of X-ray computed tomography – specifically X-ray microtomography – to reveal the morphology and petrological context of Precambrian microfossils, pseudofossils and biosedimentary structures, all of which are important in the origin and early evolution of life of Earth. The materials tested came from the Pilbara Craton of Western Australia (the 3.49 Ga Dresser Formation, the 3.46 Ga Apex chert and the 3.43 Ga Strelley Pool Formation) and the 1.88 Ga Gunflint Formation of Ontario, Canada. These units chart key developments in palaeobiology. The oldest formations contain profoundly controversial microfossil-like objects and microbially-induced sedimentary structures, whereas definitive prokaryotes are found in the youngest formations. We demonstrate that the imaging of individual microfossils and pseudofossils currently lies at the limits of the capabilities of laboratory-based X-ray microtomography and requires beneficial taphonomy. However, microtomography does provide a good overview of their petrological context at flexible spatial scales, although the quality of the data obtained from mesoscopic microbially-induced sedimentary structures and stromatolites depends largely on their style of preservation.