The role of biogenicity in the mineral world is larger than many might assume. Biological processes interact with physical and chemical processes at the Earth’s surface and far below underground, leading to the formation, for instance, of banded iron formations and manganese deposits. Microbial mats can form giant sedimentary ore deposits, which also include enrichment of further elements. Microorganisms play a basic role in catalyzing geochemical processes of the Earth and in the control, regularization and leading of cycles of elements. Microbial mats and other biosignatures can be used as indicators for environmental reconstruction in geological samples. This article reviews the many ways that microbially controlled or mediated processes contribute to mineralization and examines some published case studies for clues of what might have been missed in the analysis of sedimentary rocks when biogenicity was not taken into account. Suggestions are made for tests and analyses that will allow the potential role of biomineralization to be investigated in order to obtain a more complete view of formation processes and their implications.