Acetophenones, which show scattered distribution in organisms including phylogenetically distant plants and fungi, are play diverse roles in plant-plant, plant-insect, plant-microbiome, and even animal-insect interactions. However, the enzymes involved in plant acetophenone biosynthetic pathway remain enigmatic. Here we uncover the complete biosynthesis pathway of 4-hydroxyacetophenone glucoside using pear as a model organism. We demonstrate that the natural occurrence of 4-hydroxyacetophenone in certain pear cultivars is due to the impaired shortening reaction of propanoid side chain of 4-hydroxy-3-oxo-3-phenylpropanoyl CoA. This reaction is catalyzed by a peroxisomal 3-ketoacyl-CoA thiolase, which is homozygous malfunctioning in these pear cultivars. This rare phenomenon reminds us that not only neofunctionalization but ‘malfunctionalization’ also fuels diversification in plant secondary metabolism. Forward genetic approaches are powerful to shed light on such ‘hidden’ or recessive pathways in plants.