Green spot is a pre-harvest physiological disorder of ‘WA 38’ apple fruit that can culminate in corking immediately underneath the peel surface. Unlike bitter pit and many other corking disorders, superficial symptoms emerge in the middle of the growing season as areas of peel discoloration, with the most severe symptoms appearing as parenchyma necrosis or corking that worsens until harvest. Our previous work demonstrated the mitigative effect of early season fruit bagging on green spot appearance, but the mechanism of its onset and the biochemical signatures associated with it remained unknown. We used metabolic profiling to, first, identify metabolites associated with green spot symptoms in the peel and cortex of ‘WA 38’ apples and, then, track changes before and after disorder onset until harvest from apples that were bagged, under a shade net, or uncovered (control). We linked metabolites from multiple metabolic pathways, including carotenoids, phenolics, triglycerides, and triterpenes, with peel and cortex green spot symptoms. Many pigment and triterpene compounds associated with cortex symptoms are typically far less abundant in cortex tissue than in peel. Light-altering treatments also impacted levels of several of these compounds during the growing season; however, the inability to predict which pre-symptomatic tissue would later develop symptoms compromised the establishment of disorder genesis and latent development using this technique. Despite these challenges, we linked novel metabolites and pathways with the disorder, including those that may indicate strengthening and isolation of symptomatic tissue, possibly to provide protections similar to the fruit surface.