Tomato fruit growth and composition depend on both genotype and environment. This paper aims (i) at studying how fruit phenotypic responses to changes in carbon availability can be influenced by genotype and (ii) at identifying genotype-dependent and -independent changes in gene expression underlying variations in fruit growth and composition. To this end, we grew a parental line (S. lycopersicum) and an introgression line from S. chmielewskii harboring QTL for fresh weight and sugar content under two fruit loads (FL). Lowering fruit load increased fruit cell number and reduced fruit developmental period in both genotypes. In contrast, fruit cell size was increased only in the parental line. Modifications in gene expression were monitored in expanding fruits using microarrays and RT-qPCR for a subset of genes. FL changes induced more deployments of regulation systems (transcriptional and post transcriptional) than massive adjustments of whole primary metabolism. Interactions between genotype and FL were especially noticeable for 99 genes mainly linked to hormonal and stress responses, and on gene expression kinetics during fruit development. Links between gene expression and fruit phenotype were found for aquaporin expression levels and fruit water content, and invertase expression levels and sugar content during fruit ripening phase. In summary, the present data emphasized age- and genotype-dependent responses of tomato fruit to carbon availability, at phenotypic as well as at gene expression level.