Grape berries lose one H+ per accumulated sucrose at the inception of ripening, but the molecular mechanisms associated with this remain unknown. By investigating single fruits, we elucidated the fundamentals of the malate-sugar nexus, previously obscured by asynchrony in population-based models of ripening. The development of individual fruits was explored to capture simultaneous changes in gene expression and metabolic fluxes from flowering to overripening. Dynamics in water, tartrate, malate, hexoses, and K+ fluxes obtained by combining individual single fruit growth and concentration data, allowed us to define eleven sub-phases in fruit development, with defined groups according to RNA sequencing analysis. Co-expression network analysis revealed a range of transcript level-metabolic rate associations. A set of membrane transporters related to vacuolar over-acidification was found specifically expressed during the first growth phase. Unlike in slightly more acidic citrus, vacuolar H+-pyrophosphatase transcripts were predominantly expressed, followed by vacuolar ATPase, clarifying a thermodynamic limit beyond which their replacement by the tonoplast P3A/P3B ATPase complex is essential. Unexpectedly, expression of aluminium-activated malate transporter was low at this stage, possibly replaced by an uncharacterized anion channel. At the onset of ripening, the role of hexose transporter HT6 as a molecular switch in sugar accumulation was confirmed, electroneutralized by malate vacuolar leakage and H+ pumps activation.