AbstractThe compounds responsible for smoky and mouldy–musty off-flavours in fermented cocoa have recently been elucidated; however, their behaviour during further processing into chocolate was still unclear. The compounds 2-methoxyphenol, 3-methylphenol, 4-methylphenol, 3-ethylphenol, 4-ethylphenol, and 3-propylphenol known to contribute to smoky off-flavours showed a tendency towards a minor increase during roasting and processing into cocoa liquor. This increase amounted to 1.4-fold at the most, however, was clearly compensated by losses of 30–63% during further processing into chocolate mass and conching. Among the off-flavour compounds identified in mouldy–musty smelling cocoa, faecal, mothball-like 3-methyl-1H-indole showed a clear decrease during roasting and processing into cocoa liquor, at least at rather high roasting temperatures, and a further decrease during processing into chocolate mass and conching. In contrast, faecal, mothball-like 1H-indole substantially increased during roasting and processing into cocoa liquor, namely from concentrations below its odour threshold value to concentrations up to 8 times beyond its odour threshold value. During processing into chocolate mass and conching, 1H-indole remained virtually unchanged. The data suggested that the monitoring of off-flavour compounds at the incoming goods inspection in the chocolate industry should not be limited to the fermented beans as such but additionally include the analysis of a bean sample after test roasting to correctly assess the off-flavour potential of 3-methyl-1H-indole and 1H-indole.