Abstract By revealing that the grape berry loses one H + per accumulated sucrose at the inception of ripening, adopting a single fruit paradigm elucidates the fundamentals of the malate-sugar nexus, previously obscured by asynchrony in population-based models of ripening. More broadly, the development of the individual fruit was revisited from scratch to capture the simultaneous changes in gene expression and metabolic fluxes in a kinetically relevant way from flowering to overripening. Dynamics in water, tartrate, malate, hexoses, and K + fluxes obtained by combining individual single fruit growth and concentration data allowed to define eleven sub-phases in fruit development, which distributed on a rigorous curve in RNAseq PCA. WGCNA achieved unprecedented time resolutions in exploring transcript level-metabolic rate associations. A comprehensive set of membrane transporters was found specifically expressed during the first growth phase related to vacuolar over-acidification. Unlike in slightly more acidic citrus, H + V-PPase transcripts were predominantly expressed, followed by V-ATPase and PH5, clarifying the thermodynamic limit beyond which replacement by the PH1/PH5 complex turns compulsory. Puzzlingly, bona fide ALMT kept a low profile at this stage, possibly replaced by a predominating uncharacterized anion channel. Then, the switch role of HT6 in sugar accumulation was confirmed, electroneutralized by malate vacuolar leakage and H + pumps activation. Highlights To alleviate asynchronicity biases, transcripts showing strict coincidental timing with pericarp physiological phases were disentangled on single berries, enlightening the tight multifaceted membrane developmental control of sugar and acid fluxes.