Leaves of vines affected by the grapevine trunk disease esca complex show different degrees of severity throughout the growing season. Affected plants can still yield satisfactorily, although some berries present sclerotic spots. Little information is available on the relationship between foliar symptom severity and the quality of berries. The aim of this work was to evaluate the effect of esca complex severity on the primary metabolites of healthy berries. Berry samples were collected from healthy (control) and symptomatic vines of the white varieties Viosinho and Malvasia-fina grown 100 m apart. All plants evaluated have expressed initial symptoms in August, but showed different degrees of severity at harvest, namely chlorotic and scorched leaves (severity level 1) and tiger stripe leaves (severity level 2). The total fatty acid content was reduced in both varieties, and the reduction was mostly attributed to saturated fatty acids. On the contrary, levels of polyunsaturated fatty acids increased, probably as a defense mechanism. Among organic acids, tartaric acid levels were unchanged in Malvasia-fina, but increased with symptom progression in Viosinho; the opposite was observed for malic acid. The total free sugar content increased with symptom progression, and fructose showed the most significant variation. Varietal differences were observed in the response of amino acids, whose levels increased in Malvasia-fina and decreased in Viosinho. These varietal differences might have resulted in different degrees of host resistance, and this might explain why disease incidence and severity were more pronounced in Malvasia-fina than Viosinho.