PdAu nanocrystals are synthesised by Geobacter sulfurreducens, a dissimilatory metal-reducing bacterium, and the resulting bimetallic nanocrystal-decorated microbes are imaged using a range of advanced electron microscopy techniques. Specifically, the first example of elemental mapping of fully hydrated biological nanostructures using scanning transmission electron microscope (STEM) energy dispersive X-ray (EDX) spectrum imaging within an environmental liquid-cell is reported. These results are combined with cryo-TEM and ex situ STEM imaging and EDX analysis with the aim of better understanding microbial synthesis of bimetallic nanoparticles. It is demonstrated that although Au and Pd are colocalized across the cells, the population of nanoparticles produced is bimodal, containing ultrasmall alloyed nanocrystals with diameters < 3 nm and significantly larger core-shell structures (> 200 nm in diameter) which show higher Pd contents and exhibit a Pd enriched shell only a few nanometers thick. The application of high-resolution imaging techniques described here offers the potential to visualize the microbe-metal interface during the bioproduction of a range of functional materials by microbial "green" synthesis routes, and also key interfaces underpinning globally relevant environmental processes (e.g., metal cycling).