An organoleptic defect described as musty and/or fresh mushroom can occur in cooked apple products. GC-Olfactometry was used to characterize puree spoilage associated with sensory descriptors mushroom, cellar-like, musty, dusty or metallic. This approach, coupled with pure standards analysis allowed us to identify for the first time 1-hydroxyoctan-3-one in spoiled matrices. Using a targeted approach, 1-hydroxyoctan-3-one and octane-1,3-diol, were quantified by Stable Isotope Dilution Assay LC-MS/MS. Quantification results attested that these compounds exhibited a higher concentration in spoiled purees than in control ones and could thus be relevant markers of fruit spoilage. In a second time, the origin of 1-hydroxyoctan-3-one and octane-1,3-diol was investigated by contaminating several apple purees with specific fungal species. A Penicillium digitatum strain appeared to be the highest 1-hydroxyoctan-3-one producer, while a Botrytis cinerea strain led to a decrease of octane-1,3-diol concentration in spoiled products. It opens up avenues for the quality segmentation of fruits.