X-ray microspectroscopy is a powerful analytical method in geoscientific and environmental research as it provides a unique combination of nanoscale imaging with high spectroscopic sensitivity at relatively low beam-related sample damage. In this study, "classical"scanning transmission soft X-ray microscopy (STXM) with X-ray absorption spectroscopy and the recently established soft X-ray ptychography are applied to the analysis of selected rock varnish samples from urban and arid desert environments. X-ray ptychography enhances the spatial resolution relative to STXM by up to 1 order of magnitude. With its high chemical sensitivity, it can resolve nanoscale differences in valence states of the key varnish elements manganese (Mn) and iron. Our results emphasize the complex nanoarchitecture of rock varnish as well as the diverse mineralogy of the Mn oxy-hydroxide matrix and its embedded dust grains. In contrast to the fast-growing urban varnish, the slow-growing arid desert varnish revealed a remarkable nanoscale stratification of alternating Mn valence states, providing hints on the layer-wise and still enigmatic growth process.