Spoilage of roasted coffee products is largely suppressed through industry standards regarding storage and packaging conversely biological contamination can be attributed to cross contamination. However, the increasing trend at the upper end of the specialty coffee industry, comprising more complex (e.g., yeast inoculation and fruit infusion) and longer post-harvest processing (e.g., extended anaerobic fermentation) methods might be considered in risk for potential spoilage. Here we report the first case of mistakenly confused accumulation of mold mycelium on high end roasted Coffea arabica beans (Gesha variety from Barú, Panama, natural anaerobic process and greenhouse dried) which in turn is identified through UV/Vis spectroscopy (against a caffeine solution) as a conglomerate of needle-like caffeine crystals growing over the bean surface. Biological spoilage was unambiguously discarded through negligible microbial activity as shown through colony counting and mycotoxin analysis. Furthermore, we demonstrate that the roast degree (development time after first crack) has a significant effect on the growth of the crystals upon storage (RT and moderate light exposure). Darker roasts (70 s after first crack) showed a higher accumulation of caffeine crystals then lighter roasts (20 s after first crack), most-likely promoted through coffee oil secretion. However micro-crystal growth was already detected at lighter roasts. While uncommon in roasted beans and so far, poorly documented, crystal formation relates to increased caffeine availability at the surface through initial seed germination. Through the migration towards the endosperm surface, the xanthophyll antibacterial function is activated. A similar spoilage confusion is observed over soluble coffee granules. Yet here, crystals growth is solely related to the high caffeine concentrations. Conversely, the apparent spoilage in soluble coffee, does not have the economic burden as in high end roasted coffee and remains unrelated to any physiological process.