Archaeometrists use a variety of analytical methods to determine trace elements in ancient Greek silver coins, for provenance studies, understanding social and technological change, and authentication. One analytical problem which is little documented is understanding the horizontal spatial heterogeneity of coin elemental composition in micro-sampled areas, which are usually assumed to be uniform. This study analysed ten ancient Greek coins representative of silver circulating in the Aegean region in the sixth to third centuries BC. Scanning electron microscopy with energy dispersive spectrometry was used to map the spatial distribution of elements on coins that were abraded to remove the patina. Time of flight-secondary ion mass spectrometry was then conducted on selected coins, mapping an area ~100 × 100 µm and depth profiling from 0 to 10 µm. These data revealed the three-dimensional elemental complexity of the coins, in particular, the heterogeneity both in the patina and beneath it. These data will guide future authentication and provenance studies of larger sample sets of ancient Greek coins including the use of line scanning for laser ablation inductively coupled plasma mass spectrometry data collection rather than spot analyses, and non-destructive analytical techniques such as X-ray fluorescence spectrometry.