Indiana limestone is composed mainly of calcite and aragonite minerals, which are different crystalline forms of calcium carbonate. Due to its composition of almost pure calcium carbonate (around 97%), it is widely used in the petroleum industry as a standard porous media for laboratory experiments with a huge scope in industrial applications. A method to improve oil recovery is associated with the use of nanoparticles (NP). One of the most promising is presented to be that of silica (Si) NP, because of their compatibility with the reservoir and subsurface abundance. In this work, we applied Si NP at a concentration of 0.5%, prepared in a base fluid of 1000 ppm in crude oil, injected in Indiana limestone and tested them with microtomography (microCT) and micro x‐ray fluorescence (microXRF) techniques to evaluate the impact of the treatment. Combining morphological results with the mapping of the elements, a more complete characterization of the sample is possible for a better understanding of these interactions applied in oil field industries.