Leaf removal (LR), shoot thinning (ST) and their combination (LRST) are known to increase berry solar exposure affecting berry composition and consequently improving wine quality and antioxidant properties. We hypothesized that LR, ST or their combination (LRST) would affect flavonoid content during berry ripening by means of changes of the berry microclimate (light and temperature) as well as wine composition, quality, and antioxidant properties. Thermal time and sum of light intensity thresholds were different to achieve the maximum berry anthocyanin and flavonol contents. ST mostly affected wine characteristics by increasing alcoholic content, acidity, hue and phenolic substances. Wine antioxidant capacity decreased in ST wines likely by decreases in catechin and quercetin contents. ST and LRST increased proanthocyanidin polymerization and decreased monomeric flavan-3-ols, which may reduce wine bitterness and enhance astringency. Therefore, the management of canopy should take into account the warming trends in viticulture regions, rather than being applied preemptively.