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Abstract Biocementation is commonly based on microbial-induced carbonate precipitation (MICP) or enzyme-induced carbonate precipitation (EICP), where biomineralization of $$\text {CaCO}_{3}$$ CaCO 3 in a granular medium is used to produce a sustainable, consolidated porous material. The successful implementation of biocementation in large-scale applications requires detailed knowledge about the micro-scale processes of $$\text {CaCO}_{3}$$ CaCO 3 precipitation and grain consolidation. For this purpose, we present a microscopy sample cell that enables real time and in situ observations of the precipitation of $$\text {CaCO}_{3}$$ CaCO 3 in the presence of sand grains and calcite seeds. In this study, the sample cell is used in combination with confocal laser scanning microscopy (CLSM) which allows the monitoring in situ of local pH during the reaction. The sample cell can be disassembled at the end of the experiment, so that the precipitated crystals can be characterized with Raman microspectroscopy and scanning electron microscopy (SEM) without disturbing the sample. The combination of the real time and in situ monitoring of the precipitation process with the possibility to characterize the precipitated crystals without further sample processing, offers a powerful tool for knowledge-based improvements of biocementation.