Pyrite geochemistry has proven useful for tracking changes in the composition and physico-chemical conditions of hydrothermal fluids in ore-forming environments. Here, we investigated the microtextural features and chemical composition of pyrite, a main Au-bearing phase in the Akeshi and Kasuga deposits (Southern Kyushu, Japan), to better constrain the ore-forming processes in these high-sulfidation epithermal Au deposits. Despite the widespread distribution of Au-bearing pyrite in both deposits, no visible Au minerals coexist with pyrite. However, in situ laser ablation inductively coupled plasma mass spectrometry results show that Au concentrations in pyrite vary from below the detection limit to 41 ppm and are positively correlated with Cu (r = 0.4; up to 7400 ppm) and Bi concentrations (r = 0.44; up to 640 ppm). In both deposits, high Cu and Au concentrations occur in small (< 25 μm) anhedral grains of pyrite, which are interpreted to have rapidly crystallized from the ore-forming hydrothermal fluid. In addition, dissolution–reprecipitation textures and thin, concentric, Cu-rich overgrowths were identified in a number of larger (> 25 μm) pyrite grains and aggregates. These abrupt changes in the trace element compositions of pyrite grains likely record episodic metal-rich fluid inputs. We also propose that gold adsorption onto growing pyrite surfaces played a key role in the mineralization of these deposits.