The investigation into the flavonoids, phytoalexins, anthocyanins, and amino acids in grape berries is crucial for understanding the intricate dynamics of phytochemical composition, which significantly influences grape quality. This comprehensive study on grape berries' phytochemical composition revealed significant numerical variations across distinct phenological stages and pollinator cultivars. Notably, this work has brought to light significant variations in anthocyanidin levels corresponding to different sampling times, with EL-38 berry development stage exhibiting peak values and Bozcada Çavuşu*Vasilâki consistently showcasing the highest content at 23.95 mg/kg. The substantial increase in flavonols with sampling time was led by Bozcada Çavuşu*Vasilâki, reaching its pinnacle at EL-38 (93.86 mg/kg). Flavone content peaked at EL-38, with Vasilâki demonstrating the highest concentration (75.01 mg/kg). Flavanones exhibited an upward trend with sampling time, while catechins showed no discernible differences. Resveratrol, escalated significantly with sampling time (EL-38 > EL-37 > EL-36), and reached its zenith in Bozcada Çavuşu*Vasilâki. Phytoalexins, including pterostilbene, piceid, and viniferin, displayed substantial variations across sampling times, and reached consistently elevated in Bozcada Çavuşu*Vasilâki. Our anthocyanin analysis uncovered noteworthy variations across both sampling times and cultivars. Vasilâki consistently stood out with the highest anthocyanin content, notably in individual anthocyanins such as Peonidin-3-O-glycoside (86.71%) and Malvidin-3-O-glycoside (77.53%). Tyrosine, Proline, and Sarcosine emerged as particularly prominent, with distinct levels observed in Kuntra, Bozcada Çavuşu*Kuntra, Vasilâki, and Bozcada Çavuşu*Vasilâki. The statistical results underscored the significance of these differences, emphasizing the order of importance as Tyrosine > Proline > Sarcosine. Especially, Grapevine berry at the EL-37 exhibited the highest concentrations for Tyrosine (551.66 pmol μL−1), Serine (489.59 pmol μL−1), and Arginine (334.10 pmol μL−1). This work provides a comprehensive understanding of grape phytochemistry, shedding light on the nuanced interplay between sampling times and cultivars. The consistently superior performance of Bozcada Çavuşu*Vasilâki positions it as a cultivar of particular interest, emphasizing the relevance of our findings to the broader viticulture and grape production community.