This study provides a chemical–sensory characterization of cocoa liquors from the CCN51 variety to elucidate the molecular basis of sensory defects identified by a trained industrial panel. Samples exhibiting sourness, bitterness, astringency, and earthy notes were classified according to sensory acceptability. An integrated approach combining sensory analysis, HS-SPME-GC-MS, LC-UV/DAD, and spectrophotometric assays was applied to link volatile and non-volatile fractions with sensory perception. Sourness emerged as a multifactorial attribute resulting from the combined contribution of short-chain esters and short- to medium-chain fatty acids, likely associated with yeast activity and atypical fermentation conditions. Earthy and musty notes were not correlated with specific components, suggesting the involvement of odorants not captured by the applied analytical methods. Defective liquors showed higher levels of caffeine, total phenolics, epicatechin, and proanthocyanidins, coherently explaining increased bitterness and astringency. Overall, the findings indicate fermentation deviations as a key factor driving off-flavor development in CCN51 cocoa liquors.