The effects of canopy treatment with chitosan and the effects of the vineyard location on the quality parameters, volatile and non-volatile profiles, and sensory profile of Pinot Noir wines from South Tyrol (Italy) were studied. Multivariate statistical analysis was applied to identify the most relevant compounds associated with the variability in phenolics and anthocyanins (analyzed by UHPLC-MS), volatile components (HS-SPME-GCxGC-ToF/MS), and basic enological parameters. A clear separation of low-altitude wines (350 m.a.s.l.), which had a high concentration of most of the identified volatile compounds, compared to high-altitude wines (800 and 1050–1150 m.a.s.l.) was pointed out. Low altitude minimized the concentration of the most significant anthocyanins in wines from a valley bottom, presumably due to reduced sun exposure. Wines obtained from chitosan-treated canopies, and, more particularly, those subjected to multiple treatments per year showed a higher amount of the main non-volatile phenolics and were sensorially described as having “unpleasant flavors” and “odors”, which might suggest that grape metabolism is slightly altered compared to untreated grapevines. Thus, optimization of the treatment with chitosan should be further investigated.