The production and sustainability of grape berries with high quality and health-promoting properties is a major goal. In this regard, nano-engineered materials are being used for improving the quality and marketability of berries. In this study, we investigated the potential role of chitosan–phenylalanine nanocomposites (CS–Phe NCs) in improving the quality of Flame Seedless (Vitis vinifera L.) grape berries, such as titratable acidity (TA), pH, total soluble solids (TSS), ascorbic acid, total phenolics, total flavonoids, anthocyanin, 2,2-diphenyl-1-picryl-hydrazyl-hydrate (DPPH) radical scavenging activity, and phenylalanine ammonia-lyase (PAL) activity. In this context, grape berries collected in two growing seasons (2018–2019) were screened. Regarding the experimental design, the treatments included chitosan at a 0.5% concentration (CS 0.5%), phenylalanine at 5 mM and 10 mM concentrations (Phe 5 mM and Phe 10 mM), and chitosan–phenylalanine nanocomposites (CS–Phe NCs) at 5 mM and 10 mM concentrations. The lowest TA was recorded in grape berries treated with CS–Phe NCs with a 10 mM concentration. However, treatments enhanced with TSS, which reached the highest value with 10 mM of CS–Phe NCs, were reflected as the highest ratio of TSS/TA with 10 mM of CS–Phe NC treatment. Nanocomposites (NCs) also increased pH values in both study years compared to the control. Similarly, the ascorbic acid and total phenolic content increased in response to NP treatment, reaching the highest value with 5 mM and 10 mM of CS–Phe NCs in 2018 and 2019, respectively. The highest flavonoid content was observed with 5 mM of CS–Phe NCs in both study years. In addition, the anthocyanin content increased with 5 and 10 mM of CS–Phe NCs. PAL activity was found to be the highest with 5 mM of CS–Phe NCs in both study years. In addition, in accordance with the increase in PAL activity, increased total phenolics and anthocyanin, and higher DPPH radical scavenging activity of the grapes were recorded with the treatments compared to the control. As deduced from the findings, the coating substantially influenced the metabolic pathway, and the subsequent alterations induced by the treatments were notably appreciated due to there being no adverse impacts perceived.