In this study we establish the use of optical non-contact profilometry combined with low vacuum scanning electron microscopy (LV SEM) for the investigation of lipid surfaces. We illustrate, by using profilometry, a methodology for investigation of chocolate surface topology as a function of time, in the same area of interest. Both qualitative and quantitative data analysis has been performed for profilometry data. Further, relating these results to LV SEM images provides complementary topological information and hence a useful toolkit for the study of the chocolate surface prior and post fat bloom formation. For the demonstration of the successful combination of these two analytical techniques, white chocolate pralines were stored at two temperature-controlled conditions (at 18 °C, and cycled between 15 and 25 °C). Surface properties were then investigated during 36 weeks of storage. The surface images and the roughness parameters indicated distinct development of surface characteristics for the two storage conditions. From the results it is suggested that some imperfections, in the form of pores or protrusions, could play a role in fat bloom development and that there may be different main mechanisms of fat migration taking place for the different storage environments. In the present work, a positive correlation of profilometry data to chocolate surface characteristics and early bloom development has been established. There are indications that early prediction of fat bloom can be possible, however further work needs to be done to quantify prediction of fat bloom.