Cells, tissues, and organs harbour complex systems to allow communication between one another. The biological rhythms can be contrasting among organs, tissues, and cells, adjusting the physiology differently along the organism‘s regions. while also synchronising flowering and metabolism. Here, we revealed that Solanum lycopersicum manifests more balanced rhythms across the whole plant than wild tomatoes. Accordingly, the leaf development program is more coordinated in this organism than in wild species, in that young S. lycopersicum leaves develop slowly in comparison to mature leaves. Young leaves from wild tomatoes display higher photosynthetic rate than mature leaves, while large metabolite accumulations occur across plant segments. Consequently, diel metabolite levels are rather similar between young and mature leaves in the wild tomato S. pennellii, whereas the expression patterns for circadian clock genes are widely contrasting between differently aged leaves. We further demonstrated that introduction of domestication alleles into the wild tomato S. pimpinellifolium appears to synchronize the development of young and mature leaves, rendering this similar to that observed for S. lycopersicum. Collectively, the strengthening of inter-organ relationships in S. lycopersicum indicates an increased synchronization of its biology, which is probably fundamental to explain its elevated yield.