Anthocyanin-less (white) instead of black/red (coloured) fruits develop in grapevine cultivars without functional VviMYBA1 and VviMYBA2 genes, which conditions the colour of wines that can be produced. To evaluate whether this genetic variation has additional consequences on fruit ripening and composition, we performed microenvironment, transcriptomics and metabolomics comparisons of developing grapes between near-isogenic white- and black-berried somatic variants of Garnacha and Tempranillo cultivars. Berry temperature was up to 3.5ºC lower in white- compared to black-berried Tempranillo. An RNA-seq study combined with targeted and untargeted metabolomics revealed that ripening fruits of white-berried variants were characterized by the upregulation of photosynthesis and other light-responsive genes and their higher accumulation of specific terpene aroma precursors, fatty acid-derived aldehyde volatiles and phenylpropanoid precursor amino acids. MYBA1-MYBA2 function proved essential for flavonol trihydroxylation in black-berried somatic variants, which were also characterized by enhanced pathogen defence gene expression in berry skin and increased accumulation of C6-derived alcohol and ester volatiles and GABA. Collectively, our results indicate that anthocyanin depletion entails side effects on grape composition by altering the berry internal microenvironment and the partition of the phenylpropanoid pathway. These findings show how fruit colour can condition other fruit features, such as flavour potential and stress homeostasis.