Enzymatically Induced Calcite Precipitation (EICP) in porous media can be used as an engineering option to achieve targeted precipitation in the pore space, e.g. with the aim to seal flow paths. This is accomplished through an alteration of porosity and, consequently, permeability. A major source of uncertainty in modelling EICP is in the quantitative description of permeability alteration due to precipitation. This study investigates experimentally the time-resolved effects of growing precipitates on porosity and permeability on the pore scale in a PDMS-based micro-fluidic flow cell. The experimental methods are explained; these include the design and construction of the micro-fluidic cells, the preparation and usage of the chemical solutions, including the injection strategy, and the monitoring of pressure drops at given flux rates to conclude on permeability. Imaging methods are explained with application to EICP, including optical microscopy and X-Ray micro-Computed Tomography (XRCT) and the corresponding image processing and analysis. We present and discuss detailed experimental results for one particular micro-fluidic set-up as well as the general perspectives for further experimental and numerical simulation studies on induced calcite precipitation. The results of the study show the enormous benefits and insights of combining both light microscopy and XRCT with hydraulic measurements in micro-fluidic devices. This allows for a quantitative analysis of the evolution of precipitates with respect to their size and shape, while monitoring the influence on permeability. We can demonstrate that we improved the interpretation of monitored flow data dependent on changes in pore morphology.